This study investigated the effect of ultrasound-assited cooking on the migration of nutritional components, flavor formation, and stability of Larimichthys crocea fillet soup. The results showed that ultrasonic assistance shortened the cooking time while improving the quality of the fish soup. The soup prepared with ultrasonic treatment for 80 min (U80) was comparable to that of the soup prepared by conventional cooking for 120 min (C120) in terms of taste, fat content, and whiteness. The fish soup prepared with ultrasonic treatment at 800 W for 120 min received a sensory score of 8.40 and an umami response value of 4.15, demonstrating optimal flavor quality. It was further found that high-intensity ultrasound (800 W, 120 min) did not significantly affect the dissolution of soluble proteins, nucleotides or oligopeptides, but significantly increased the contents of umami amino acids and fat by 3.85% and 29.09%, respectively, compared with the control. In addition, ultrasonic treatment effectively reduced the particle size of protein-lipid nanoparticles, increased the concentration of nanoparticles, and inhibited their agglomeration during the stewing process, thereby reducing the surface tension and friction coefficient of the soup system and enhancing its emulsion stability and smoothness. In conclusion, ultrasonic-assisted stewing shows application potential in enhancing the taste quality and stability of L. crocea fillet soup, offering an energy-efficient approach for the utilization and industrial processing of fish by-products.