Background Polydactyly of the foot is one of the most frequent anomalies of the limbs. However, most classification systems are based solely on morphology and tend to be inaccurate and less relevant to surgical methods and results. The purpose of this study is to present our new classification of polydactyly of the foot, which can serve as a predictor of treatment and prognosis. Methods To find a correlation between the various morphologic traits of polydactyly of the foot and the treatment plan and outcomes, we reviewed 532 cases of polydactyly of the foot in 431 patients treated in our hospital, expanding on our previous study that described polydactyly based on the importance of metatarsal bone status and varus deformity. The records of patients were evaluated and compared with previous studies at other centers. Results Unsatisfactory results were seen in 36 cases, which included 5 cases of incomplete separation due to syndactylism, 23 cases of axis deviation, and 8 cases of remnants of extra-digit metatarsal bones. The locus of the polydactyly, or the digit which was involved, did not seem to affect the final postoperative outcomes in our study. Three factors-syndactylism, axis deviation, and metatarsal extension-are the major factors related to treatment strategy and prognosis. Therefore, we developed a new classification system using three characters (S, A, M) followed by three groups (0, 1, 2), to describe the complexity of polydactyly of the foot, such as S₁A₂M₂. Conclusions Our new classification could provide a communicable description to help determine the surgical plan and predict outcomes.