Ultrasound-assisted freezing (UAF) has been proved to be a new technology to improve the quality of frozen foods. Frequency is an important parameter affecting UAF result. This study was to investigate the effects of single-, dual- and multi-frequency UAF on muscle quality and myofibrillar protein structure in large yellow croaker (Larimichthys crocea), providing reference for the application of multi-frequency UAF in frozen foods. Multi-frequency UAF increased the freezing rate and had lower thawing loss, thiobarbituric acid reactive substances (TBARS) value, total volatile basic nitrogen (TVB-N) value, and higher immobilized water content. Multi-frequency UAF had lower carbonyl, higher sulfhydryl content, and more stable myofibrillar protein secondary and tertiary structures. Confocal laser scanning microscopy (CLSM) indicated that the filamentous polymer in muscle fibrin solution with multi-frequency UAF was transformed into more evenly distributed units. In general, multi-frequency UAF significantly improved the freezing rate, reduced lipid oxidation, and maintained the myofibrillar structure.