Wedge-heeled shoes, which are formed by elevating both the forefoot and heel, have been popular among young women. However, research on the foot shape in wedge-heeled shoes is lacking. This study aimed to access the effects of forefoot height (10, 20, and 30 mm) and heel height (30, 50, 70, and 90 mm) on foot shape and perceived comfort when wearing wedge-heeled shoes. Three-dimensional (3D) foot scanning was performed on 35 females and the 14 foot dimensions were measured. Increased forefoot height generated larger lengths (foot, ball and out ball), smaller girths (ball and instep) and heights (instep and navicular) (p < 0.05). Thus, when the forefoot height increased, the foot became longer, slimmer and flatter. Moreover, elevated heel height resulted in larger dimensions for girths (ball and instep), heights (instep and navicular), and smaller dimensions for lengths (foot, ball and out ball), widths (diagonal and horizontal) and toe 5 angles of the foot (p < 0.01). That means shorter, narrower and more convex foot shapes were observed when heel height increased. Subjective measurements implied that increased forefoot height significantly enhanced perceived comfort, whereas increased heel height diminished comfort. It was found that forefoot elevation could result in less deformation and discomfort which accompanied heel elevation, especially in the low heel-toe drop combinations (10 × 30 and 20 × 30 mm). The findings provide valuable references for enhancing shoe fitting and comfort for wedge-heeled shoes by providing dimensional data on the toe, ball, arch and instep regions.