Sea cucumber intestinal peptide has antioxidant, anti-cancer and anti-fatigue effects, while the strong fishy smell restricts its application in food industry. In this study, watermelon essence was entrapped into V-type crystalline starch using solid encapsulation method. The inclusion complex (IC) was characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). Meanwhile, the IC was added to sea cucumber intestinal peptide, and the flavor of mixed samples stored at different temperatures (4, 25, 50 °C) were investigated. The results showed that the natural watermelon flavor was introduced into V-type crystalline starch, and the encapsulation rate of IC was 63.8% (W/W). Compared with V-type crystalline starch, the crystallinity of IC decreased from 39.5% to 28.9%, and the enthalpy value was 13.0 J/g. The intensities of peak at 1 023 and 1 158 cm⁻¹ were significantly lower than those of V-type crystalline starch, and the characteristic peak of C-H bending vibration at 856 moved to 839 cm⁻¹. The electronic nose and sensory analysis showed that the watermelon flavor stored at different temperatures exhibited controlled release characteristics. The IC could mask the odor of sea cucumber peptide and give samples a fruity flavor, thereby enhancing the acceptability of consumers. In conclusion, natural watermelon flavor has been successfully encapsulated in V-type crystalline starch, and can effectively improve the flavor of intestinal peptides and prolong the flavor retention time of the essence. These results will enrich and develop the flavor quality improvement theory of aquatic products, and provide the theoretical reference for high-value application of aquatic products.