Insoles play an important role in the conservative treatment of functional flat foot. The features of 3D-printed insoles are high customizability, low cost, and rapid prototyping. However, different designed insoles tend to have different effects. The study aimed to use 3D printing technology to fabricate three different kinds of designed insoles in order to compare the biomechanical effects on the lower extremities in flat foot participants. Ten participants with functional flat foot were recruited for this study. Data were recorded via a Vicon motion capture system and force plates during walking under four conditions: without insoles (shoe condition), with auto-scan insoles (scan condition), with total contact insoles (total condition), and with 5-mm wedge added total contact insoles (wedge condition). The navicular height, eversion and dorsiflexion angles of the ankle joint, eversion moment of the ankle joint, and adduction moment of the knee joint were analyzed, and comfort scales were recorded after finishing the analysis. Compared to the shoe condition, all three 3D printed insoles could increase the navicular height and ankle dorsiflexion angle and improve comfort. Among the three insoles, the wedge condition was the most efficient in navicular height support and increasing the ankle dorsiflexion angle.