[Objective] The purpose of this study was to confirm the effectiveness of a new functional exercise method for the rehabilitation of athletes after surgical treatment for accessory navicular syndrome. [Methods] In this study, a total of 38 patients were recruited from 2017 to 2020 ,they were randomly divided into two groups. The same surgical method and different functional exercise method were used to compare the postoperative functional recovery of the two groups. [Results] The operation and follow-up were completed successfully in both groups.There was no significant difference in VAS scores, AOFAS scores, Maryland scores and EMG between the two groups before different functional exercise methods were used. After 3 months of functional exercise, there were statistically significant differences in scale scores, EMG and foot activity ability between the two groups (P<0.05).[Conclusion] This new functional exercise method can effectively improve the functional recovery of athletes after accessory navicular surgical, it is worth promoting.