To compare the effectiveness of subtalar arthroereisis (STA) combined with modified Kidner procedure versus STA alone in the treatment of flexible flatfoot combined with painful accessory navicular bone in children. The clinical data of 33 children with flexible flatfoot combined with painful accessory navicular bone who were admitted between August 2018 and August 2021 and met the selection criteria were retrospectively analyzed. They were divided into a combination group (17 cases, treated by STA combined with modified Kidner procedure) and a control group (16 cases, treated by STA alone) according to the surgical methods. There was no significant difference in baseline data between the two groups ( P>0.05), such as gender, age, affected side of the foot, disease duration, and preoperative visual analogue scale (VAS) score, American Orthopaedic Foot and Ankle Society (AOFAS) ankle-hindfoot score, talus-first metatarsal angle (T1MT), talus-second metatarsal angle (T2MT), talonavicular coverage angle (TCA), talus first plantar angle (Meary angle), calcaneal inclination angle (Pitch angle), and heel valgus angle (HV). The operation time, incision length, intraoperative blood loss, number of intraoperative fluoroscopies, and perioperative complications were recorded in both groups. The anteroposterior, lateral, and calcaneal axial X-ray films for the affected feet were taken regularly, and T1MT, T2MT, TCA, Meary angle, Pitch angle, and HV were measured. The VAS score, AOFAS ankle-hindfoot score were used to evaluate pain and functional recovery before and after operation. Surgeries in both groups were successfully performed without surgical complication such as vascular, nerve, or tendon injuries. Less operation time, shorter incision length, less intraoperative blood loss, and fewer intraoperative fluoroscopies were found in the control group than in the combination group ( P<0.05). One case in the combination group had partial necrosis of the skin at the edge of the incision, which healed after the dressing change and infrared light therapy, and the rest of the incisions healed by first intention. All children were followed up 12-36 months, with a mean of 19.6 months. At last follow-up, VAS score and AOFAS ankle-hindfoot score significantly improved in both groups when compared with preoperative ones ( P<0.05), and the differences of these scores between before and after operation improved more significantly in the combination group than in the control group ( P<0.05). Imaging results showed that the T1MT, T2MT, TCA, Meary angle, and HV significantly improved in both groups at last follow-up when compared with preoperative ones ( P<0.05), and the Pitch angle had no significant difference when compared with preoperative one ( P>0.05). But there was no significant difference in the difference of these indicators between before and after operation between the two groups ( P>0.05). Both procedures are effective in the treatment of flexible flatfoot children with painful accessory navicular bone. STA has the advantage of minimally invasive, while STA combined with modified Kidner procedure has better effectiveness.