Giant freshwater prawn (Macrobrachium rosenbergii) is valued for its tender taste and high nutritional value, but its rapid post-mortem spoilage calls for effective preservation methods. Vacuum freeze-drying is ideal for maintaining product quality via low-temperature dehydration, yet its large energy consumption and long processing time limit its widespread use. Physical field pretreatments have recently become a promising way to modify food matrices before drying, which may improve drying efficiency and shape the final product’s quality. This study systematically explored how different physical field pretreatments affect protein oxidation, structural changes, and in vitro gastrointestinal digestion of myofibrillar proteins in freeze-dried prawn. Boiled prawn samples were treated with three protocols before freeze-drying， microwave pretreatment (MF, 280 W for 90 s), ultrasound pretreatment (UF, 40 kHz, 90 W for 30 min), and combined ultrasound-microwave pretreatment (UMF, ultrasound followed by microwave). The freeze-dried prawn samples were subjected to in vitro gastrointestinal digestion using simulated gastric and intestinal fluids, and their myofibrillar proteins were extracted during and after digestion to test for oxidation indicators (sulfhydryl and carbonyl contents) and structural features (secondary structure by Raman spectroscopy, tertiary conformation by fluorescence spectroscopy, surface hydrophobicity by bromophenol blue binding). Digestive results were evaluated by digestibility, hydrolysis degree, peptide profiles, particle size distribution, SDS-PAGE patterns, and confocal laser scanning microscopy; the antioxidant capacity of final digests was measured via ABTS and hydroxyl radical scavenging assays. Relative to the control group, all physical field pretreatments significantly promoted protein oxidation (P < 0.05), as evidenced by reduced sulfhydryl groups and elevated carbonyl contents. The combined UMF treatment induced the highest carbonyl levels, indicating a synergistic oxidative effect. Each pretreatment elicited distinct conformational changes in myofibrillar proteins, which in turn governed their subsequent digestive behavior. The MF group exhibited a marked conversion to β-sheet structure (27%), indicative of compact aggregate formation driven by enhanced hydrophobic interactions and possible covalent crosslinking. This was corroborated by pronounced fluorescence quenching and a moderate increase in surface hydrophobicity. In contrast, the UF group displayed the most extensive structural unfolding, characterized by the lowest βsheet content (20%), a substantially elevated βturn proportion, and the highest surface hydrophobicity—reflecting a loose and flexible conformation with readily accessible hydrophobic residues. The UMF group occupied an intermediate structural state: while αhelix content declined comparably across treatments, its βsheet level (22%) remained similar to the control, yet it achieved the highest βturn proportion (51%). Its surface hydrophobicity and fluorescence intensity fell between those of the UF and MF groups, indicating that prior ultrasound exposure mitigated the aggregative effects of subsequent microwave treatment. These structural variations directly dictated digestive outcomes. The compact βsheet architecture of MF proteins severely hindered pepsin accessibility, leading to the lowest gastric digestibility and degree of hydrolysis. Conversely, the unfolded conformation of UF proteins facilitated enzyme penetration, yielding the highest gastric digestibility (43.13%) while maintaining a hydrolysis degree (6.05%) comparable to the control. Notably, the UMF group demonstrated significantly enhanced gastric digestibility and hydrolysis relative to the MF group. Following complete gastrointestinal digestion, the UF group retained the highest overall digestibility (85.56%, P < 0.05), yet its final degree of hydrolysis (15.19%) was significantly lower than that of the control. All pretreatments significantly enhanced the antioxidant activity of the final gastrointestinal digests (P < 0.05). Specifically, the UMF group exhibited the highest ABTS radical scavenging activity, while the UF group demonstrated superior hydroxyl radical scavenging capacity.0.05), with UMF having the highest ABTS scavenging activity and UF superior hydroxyl radical scavenging. In conclusion, this investigation establishes that ultrasound, microwave, and their combination distinctly modulate myofibrillar protein structure in freeze-dried prawn, thereby governing subsequent gastrointestinal fate through oxidation-state-dependent conformational pathways. Microwave-induced thermal aggregation, characterized by elevated β-sheet content and compact architecture, severely compromises protein digestibility by restricting enzyme access to cleavage sites. Ultrasound-induced structural unfolding, while significantly enhancing initial enzyme accessibility and overall digestibility through increased surface hydrophobicity and flexible conformations, may ultimately limit hydrolysis depth due to associated oxidative modifications. Notably, the combined ultrasound-microwave pretreatment (UMF) induces a favorable intermediate protein state, featuring elevated β-turn content, moderate β-sheet levels, and balanced surface hydrophobicity. This intermediate state effectively balances processing efficiency and nutritional quality by alleviating microwave-induced protein aggregation while retaining the ultrasound-enabled structural accessibility of proteins, ultimately enhancing digestibility and facilitating the release of bioactive antioxidant peptides. This study provides a theoretical basis for developing high-quality freeze-dried aquatic products through targeted physical field pretreatments.