Background Amputation is commonly performed for toe necrosis secondary to peripheral vascular diseases, such as diabetes mellitus. When amputating a necrotic toe, preservation of the bony structure is important for preventing the collapse of adjacent digits into the amputated space. However, in the popular terminal Syme’s amputation technique, partial amputation of the distal phalanx could cause increased tension on the wound margin. Herein, we introduce a new way to resect sufficient bony structure while maintaining the normal length, based on a morphological analysis of the toes. Methods Unlike the pulp of the finger in the distal phalanx, the toe has abundant teardrop-shaped pulp tissue. The ratio of the vertical length to the longitudinal length in the distal phalanx was compared between the toes and fingers. Amputation was performed at the proximal interphalangeal joint level. Then, a mobilizable pulp flap was rotated 90° cephalad to replace the distal soft tissue defect. This modified toe fillet flap was performed in 5 patients. Results The toe pulp was found to have a vertically oriented morphology compared to that of the fingers, enabling length preservation through cephalad rotation. All defects were successfully covered without marginal ischemia. Conclusions While conventional toe fillet flap coverage focuses on the principle of length preservation as the first priority, our modified method takes both wound healing and length into account. The fattiest part of the pulp is advanced to the toe tip, providing a cushioning effect and enough length to substitute for phalangeal bone loss. Our modified method led to satisfactory functional and aesthetic outcomes.