Objective To investigate the feasibility and application value of digital technology in establishing the micro-vessels model of cross-boundary perforator flap in rat. Methods Twenty 8-week-old female Sprague Dawley rats, weighing 280-300 g, were used to established micro-vessels model. The cross-boundary perforator flaps of 10 cm×3 cm in size were prepared at the dorsum of 20 rats; then the flaps were suturedin situ. Ten rats were randomly picked up at 3 and 7 days after operation in order to observe the necrosis of flap and measure the percentage of flap necrosis area; the lead-oxide gelatin solution was used for vessels perfusion; flaps were harvested and three-dimensional reconstruction of micro-vessel was performed after micro-CT scanning. Vascular volume and total length were measured via Matlable 7.0 software. Results The percentage of flap necrosis area at 3 days after operation was 19.08%±3.64%, which was significantly lower than that at 7 days (39.76%±3.76%;t=10.361, P=0.029). Three-dimensional reconstruction via the micro-CT clearly showed the morphological alteration of micro-vessel of the flap. At 3 days after operation, the vascular volume of the flap was (1 240.23±89.71) mm3 and the total length was (245.94±29.38) mm. At 7 days after operation, the vascular volume of the flap was (1 036.96±88.97) mm3 and the total length was (143.20±30.28) mm. There were significant differences in the vascular volume and the total length between different time points (t=5.088, P=0.000; t=7.701, P=0.000). Conclusion The digital technology can be applied to visually observe and objectively evaluate the morphological alteration of the micro-vessels of the flap, and provide technical support for the study of vascular model of flap.