Acute hepatopancreatic necrosis disease （AHPND） is one of the most severe bacterial diseases in the culture of shrimp and is primarily associated with toxigenic Vibrio species （e.g., V. parahaemolyticus, V. harveyi, V. owensii and V. campbellii） carrying pirA/pirB toxin–encoding plasmids. Disease outbreaks are typically accompanied by hepatopancreatic damage and disruption of the host-associated microbiota, which markedly increases disease risk under intensive production conditions and results in substantial economic losses to the global shrimp aquaculture industry. Although the serious impact of AHPND on shrimp farming has been widely recognized, effective control at the production level remains challenging. Current prevention and control measures largely rely on empirical husbandry practices or the application of single products, whereas system-level and clinically oriented intervention technologies that can be directly implemented under commercial farming conditions are still notably lacking. This limitation is particularly evident in intensive aquaculture systems, where disease management requires integrated strategies that are precise, efficient, reproducible, and compatible with routine production operations. Here, we evaluated an integrated “compound traditional Chinese medicine + Compound probiotic agent” strategy under commercial pond conditions. Four hydrologically isolated ponds were included and assigned to two management regimes to assess performance across contrasting production loads: a low-density/high-feeding regime (G1/G2) and a high-density/low-feeding regime (G3/G4). The intervention consisted of administering a functional diet formulated with a laboratory-developed additive on days 0 and 7, combined with supplementation using a Bacillus-dominant compound probiotic; routine feeding followed standard farm practice on the remaining days, consistent with a field-applicable pulsed dosing schedule. System-level responses were quantified using a suite of production-relevant indicators, including nitrogenous water-quality variables, hepatopancreatic pathogen load, shrimp non-specific immune enzyme activities, culture-based bacterial and Vibrio loads in pond water and shrimp, histological observations, and intestinal microbiome profiles obtained by 16S rRNA gene sequencing. Under different culture load conditions, shrimp tissues remained structurally intact, with no signs of shrimp vibriosis.Salinity and pH remained stable throughout monitoring (salinity ranged from 1.96 to 2.41 ppt at site 1 and from 2.85 to 2.91 ppt at site 2; pH ranged from 8.1 to 8.5), and temperature and dissolved oxygen exhibited expected diel variation. Against this relatively stable physicochemical background, nitrogen-related parameters responded rapidly to the intervention. Following dosing, ammonia nitrogen (NH?-N) and nitrite nitrogen (NO?-N) consistently showed a rapid decline followed by stabilization: in the low-density/high-feeding ponds, NH?-N decreased from 0.22-0.29 mg/L to 0.10 mg/L within 2 days and remained stable, while NO?-N declined from 0.82-0.97 mg/L to 0.49-0.62 mg/L within 4 days; in the high-density/low-feeding ponds, NH?-N decreased from 0.42-0.52 mg/L to 0.10-0.23 mg/L within 4 days, and NO?-N in both ponds decreased and stabilized within 2 days. In parallel, multiple innate immune enzymes increased after dosing, including phenoloxidase, lysozyme, acid phosphatase, and alkaline phosphatase (PO increased by 30-39% within 4 days at site 1 and by 41-57% at site 2; LZM increased by 1-2 fold within 3 days at site 1 and by 2-9 fold within 4 days at site 2; ACP increased by 1-1.5 fold within 2 days; AKP increased by 10 fold within 2 days), whereas superoxide dismutase decreased, which may indicate reduced oxidative-stress demand in conjunction with lower microbial pressure and improved nitrogen status. qPCR analysis further showed that the AHPND pathogen load in shrimp hepatopancreas followed a common pattern in all four ponds, with high initial levels at day 0, a marked decline at day 2, and a rebound at day 6. Culture-based enumeration corroborated a pronounced short-term suppression of microbial loads: within 2 days, total cultivable bacteria and cultivable vibrios decreased in both water and shrimp, with maximum reductions of 7.14×103 CFU/mL (water bacteria) and 1.28×103 CFU/mL (water vibrios), and 2.72×10? CFU/mL (shrimp-associated bacteria) and 2.32×103 CFU/mL (shrimp-associated vibrios). Water Vibrio counts declined to 18-40 CFU/mL, and Vibrio proportions decreased to low single digits (2-9% in water and ≤2% or <1% in shrimp, depending on pond). Microbial loads subsequently rebounded; by day 6, both total bacteria and vibrios had increased by approximately one order of magnitude and approached baseline levels, consistent with transient suppression followed by recovery. Microbiome sequencing indicated that the intervention did not override pond-specific baseline community structure: principal component analysis clustered samples primarily by pond, and samples from days 2, 4, and 6 post-application within each pond clustered closely, suggesting bounded temporal variation rather than a regime shift. At the phylum level, intestinal microbiota were dominated by Bacillota and Actinobacteriota, with contributions from Pseudomonadota, Cyanobacteriota, Chloroflexota, and Chlamydiota; at the genus level, ponds exhibited distinct dominant assemblages but shared a substantial core (383 genera; 35.5%). LEfSe further identified discriminatory taxa that may serve as candidate biomarkers for monitoring and for refining application timing and dosage. No AHPND-associated clinical signs were observed during the monitoring period, and survival performance was acceptable. Collectively, the coordinated improvements in nitrogen control, enhancement of key innate immune activities, and transient reduction in Vibrio pressure support a synergistic stabilization effect of the functional diet and Bacillus-based probiotic on the pond environment and host-microbiome system. The two-dose schedule (day 0 initiation and day 7 reinforcement) and the observed 2-4 day response window offer operationally actionable guidance for integration into routine farm management, particularly when coupled with ammonia/nitrite monitoring and simple Vibrio plate counts to inform re-application. Overall, this field evaluation across contrasting culture intensities indicates that the “compound traditional Chinese medicine + Compound probiotic agent” strategy can attenuate nitrogen peaks, reduce hepatopancreatic pathogen load, enhance innate immune indicators, transiently suppress Vibrio pressure, and preserve pond-specific microbiome stability, providing a practical basis for scalable, antibiotic-sparing AHPND prevention and control.