From a subject group of pes cavus, the purpose of this study was to evaluate the biomechanical characteristics of lower limbs, based on plantar foot pressure and electromyography (EMG) activities, by the effects on two kind of custom-made insoles. Ten individuals among thirty females with a clinical diagnosis of idiopathic pes cavus (mean age (SD): 22.3 (0.08) years) were selected for the study. The plantar foot pressure data and EMG activities of four lower limb muscles were collected, when subjects walked on a treadmill, under three different experimental conditions. The plantar foot pressure data was analyzed, after the bilateral foot was divided into three areas of masks and into four sections of stance phase, to compare plantar foot pressure. The EMG activities were analyzed for integrated EMG (IEMG) value. The results show that plantar foot pressure concentrated in particular parts is decreased by custom-made insoles. In the case of EMG, all the muscle activities decreased significantly. The custom-made insoles dispersed pressure concentrated by the higher medial longitudinal arch and improved the efficient use of muscles. In particular, the extension structure in the forefoot of custom-made insoles was more efficient for pes cavus. Therefore, it could help patients to walk, by offering support to prevent the disease of pes cavus deformity, and to relieve the burden and fatigue in the lower limbs on gait.