Objective To study topological structure of a new type of three-dimensional (3D) printed height increasing insoles for leg length discrepancy (LLD) and its effect on biomechanics of lower limbs. Methods Topological structure for middle and rear part of the insole was optimized by solid isotropic microstructures with penalization (SIMP), the force was loaded and the boundary conditions were set according to force area of the insole, and the height increasing insole with thermoplastic polyurethanes (TPU) materials was printed by selected laser sintering (SLS). The insoles were used in 9 patients with LLD, visual analogue scale (VAS) and Maryland foot function scores were used to compare pain and foot function changes of patients before and after using the insole, and the 3D gait analysis system was used to compare spatiotemporal parameters and vertical ground reaction force (vGRF) of both lower limbs. Result sAfter the patient wore 3D printed insole, VAS scores decreased, Maryland foot function scores increased, vGRF of both lower limbs decreased, and the difference of cadence, stance phase and swing phase in both lower limbs decreased. Conclusions The 3D printed height increasing insole after topology optimization can improve coordination of lower limb movement, reduce ground impact, relieve pain and improve foot function, thus providing an effective personalized orthopedic plan for LLD treatment in clinic.