Abstract: The fishy off-flavor compounds generated during the preparation of sea cucumber peptides severely compromise product flavor and application. Conventional deodorization technologies suffer from limitations such as incomplete deodorization and easy damage to bioactive components. Therefore, developing efficient, mild, and green deodorization technologies is key to promoting the high-value utilization of sea cucumber peptides. In this study, we used body wall waste of Apostichopus japonicus as raw material, sea cucumber peptides were prepared by microwave-assisted papain hydrolysis, followed by deodorization using ozone oxidation. The optimal process conditions for both dry and wet processes, as well as their effects on fishy off-flavor compounds and nutritional components, were investigated. Through single-factor and orthogonal experiments, we optimized key parameters and comprehensively evaluated deodorization efficiency using sensory evaluation, Headspace Soild-Phase Microextraction combined with Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS), and nitrogen content analysis. Results demonstrate that the optimal conditions for the dry method were 70% ozone concentration with 120 min reaction time, achieving a fishiness intensity value of 2.5. For the wet method, the optimal conditions were 70% ozone concentration, 20 min reaction time, and 35 °C reaction temperature, reducing the fishiness intensity value to 1.9. HS-SPME-GC-MS analysis revealed that the wet method completely eliminated dimethyl trisulfide and significantly reduced 2,4-di-tert-butylphenol content, although certain aldehydes (Nonanal and decanal) showed slight increases. In contrast, the dry method effectively reduced fishy compounds while preventing aldehyde generation. Nitrogen content analysis indicates that ozone treatment had no significant impact on the total and amino nitrogen contents of sea cucumber peptides, confirming well-preserved protein nutritional quality. The study provides an efficient and mild deodorization approach for the high-value utilization of sea cucumber peptides, demonstrating promising application prospects.