Objective To explore the relationship between shoe comfort and foot loading characteristics in two types of basketball shoe during different basketball footwork. Methods Two Kistler 3D force platforms and Medilogic insole plantar pressure system were used to collect the kinetic data of 12 healthy male basketball players wearing two types of basketball shoe (shoe L and shoe N) during three varieties of basketball footwork (side-step cutting, 90° varied-direction running, lay-up), including peak impact force, peak loading rate, and peak plantar pressure. The perception test scale was used to evaluate comfort for two types of basketball shoe during three kinds of basketball footwork. Results For the two types of basketball shoes, there was no significantly difference in the impact force during the three kinds of basketball footwork, but the plantar pressure of shoe L was significantly greater than that of shoe N during side-step cutting and lay-up. Shoe N was significantly more comfortable than shoe L, with a significant difference in preference (heel stability, heel responsiveness, forefoot cushioning, heel cushioning, and overall liking) and intensity (forefoot and heel cushioning) on a dynamic scale. Conclusions The plantar pressure and comfort show significant differences in the two types of shoes; however, none of the shoes appeared definitively superior in the two evaluations. It is suggested that the biomechanical characteristics of the shoes and the subjective evaluation of the athletes should be considered in the overall design and evaluation of specialized shoes.