Genipin is a natural crosslinker that improves the functional properties of proteins by modifying its structures. This study aimed to investigate the effects of sonication on the emulsifying properties of different genipin concentration-induced myofibrillar protein (MP) cross-linking. The structural characteristics, solubility, emulsifying properties, and rheological properties of genipin-induced MP crosslinking without sonication (Native), sonication before crosslinking (UMP), and sonication after crosslinking (MPU) treatments were determined, and the interaction between genipin and MP were estimated by molecular docking. The results demonstrated that hydrogen bond might be the main forces for genipin binding to the MP, and 0.5 μM/mg genipin was a desirable concentration for protein cross-linking to improve MP emulsion stability. Ultrasound treatment before and after crosslinking were better than Native treatment to improve the emulsifying stability index (ESI) of MP. Among the three treatment groups at the 0.5 μM/mg genipin treatment, the MPU treatment group showed the smallest size, most uniform protein particle distribution, and the highest ESI (59.89%). Additionally, the highest α-helix (41.96%) in the MPU + G5 group may be conducive to the formation of a stable and multilayer oil–water interface. Furthermore, the free groups, solubility, and protein exposure extent of the MPU groups were higher than those of UMP and Native groups. Therefore, this work suggests that the treatment of cross-linking followed by ultrasound (MPU) could be a desirable approach for improving the emulsifying stability of MP.