As marine industrialization accelerates, anthropogenic underwater noise has emerged as a pervasive environmental stressor, significantly altering the "Anthropocene ocean soundscape." Among emerging noise sources, deep-sea aquaculture vessels characterized by continuous, low-frequency mechanical emissions present a unique but poorly understood threat to wild marine animals and cultured species. This study systematically evaluated the impact of aquaculture vessel noise (200-1000 Hz) on the large yellow croaker (Larimichthys crocea), a species of high economic value and vocal sensitivity. By integrating behavioral observations, physiological assays, and brain transcriptomics, we characterized the frequency-dependent and time-dependent responses of L. crocea to sustained acoustic stress. The experimental design utilized five noise frequency groups (200, 400, 600, 800, and 1000 Hz) at a constant sound pressure level of 100 ± 2 dB, with sampling conducted across seven time points up to 24 h. Behavioral results indicated that all noise frequencies initially triggered acute stress, evidenced by significant increases in swimming speed, tail-beat frequency, and opercular beat rate. However, while individuals in the 200-600 Hz groups demonstrated behavioral habituation and returned to baseline levels within 24 hours, those in the 800 Hz and 1000 Hz groups remained in a state of heightened activity, indicating the onset of chronic stress. Physiological analysis corroborated these behavioral trends. Specifically, 800 Hz and 1000 Hz noise exposure triggered sustained elevations in serum cortisol and adrenaline levels, signaling prolonged activation of the hypothalamus-pituitary-interrenal (HPI) axis and the sympathetic-adrenal medulla system. In contrast, lower frequency treatments (200-400 Hz) did not induce significant long-term changes in these stress biomarkers. Glucose levels exhibited transient spikes in the 800 Hz group during early exposure, likely to mobilize energy for "fight or flight" responses, before stabilizing. To elucidate the molecular mechanisms underlying these responses, transcriptomic profiling was performed on brain tissues from the 800 Hz and 1000 Hz groups. We identified 3,668 and 1,107 differentially expressed genes (DEGs) in the 800 Hz and 1000 Hz treatments, respectively. Functional enrichment analysis revealed that both frequencies significantly perturbed calcium signaling pathways, leading to potential intracellular calcium overload and excitotoxicity. To mitigate this, brain tissues exhibited an adaptive but costly downregulation of oxidative phosphorylation related genes to reduce reactive oxygen species (ROS) production, alongside a systemic upregulation of extracellular matrix (ECM) remodeling genes to repair neural damage. Notably, the two sensitive frequencies induced distinct forms of cellular injury: 800 Hz noise primarily activated TNF-α-mediated neuroinflammation and pro-apoptotic pathways, while 1000 Hz noise significantly suppressed DNA repair mechanisms and protein homeostasis, potentially impairing cognitive and memory functions. In conclusion, our findings demonstrate that L. crocea is particularly vulnerable to aquaculture vessel noise in the 800-1000 Hz range. Chronic exposure at these frequencies leads to multi-level physiological exhaustion, metabolic suppression, and structural remodeling of the central nervous system. These results provide a critical scientific basis for the acoustic design of deep-sea aquaculture platforms, suggesting that noise mitigation strategies should specifically target the 800-1000 Hz frequency band to safeguard fish welfare and the sustainability of the aquaculture industry.