Rusa unicolor and Budorcas taxicolor are national key protected wildlife in China. Understanding the spatial distribution pattern and the habitats utilization of endangered species is a priority for developing the appropriate protection and management strategies. In this paper, the data based on the entity, feces and traces of Rusa unicolor and Budorcas taxicolor were collected with the infrared cameras and line transect method in Anzihe protected areas of Sichuan Province. Based on 124 valid sites of Rusa unicolor and 79 valid sites of Budorcas taxicolor, and combined with 15 environmental variables, the habitat suitability of Rusa unicolor and Budorcas taxicolor in the protected areas was evaluated by MaxEnt model. The results suggested that: (1) the evaluation results of habitat suitability of Rusa unicolor and Budorcas taxicolor reached a good level, and their Area Under Curve (AUC) values were 0.888 and 0.813, respectively. (2) The suitable and relatively suitable habitats of Rusa unicolor were mainly distributed in the middle and south part of the protected areas, with altitudes ranging from 1474 to 3336 m, and the areas were 943.23 hm² and 3390.15 hm², respectively, accounting for 6.25% and 22.48% of the total protected areas. (3) The main sites of suitable and relatively suitable habitats of Budorcas taxicolor were mainly distributed in the middle and western part of the protected areas, where altitudes ranged between 1467 to 3823 m, and the areas were 1808.37 hm² and 8384.35 hm², respectively, accounting for 11.99% and 55.59% of the total protected area. (4) The ecological overlap index of Rusa unicolor and Budorcas taxicolor was comparatively high,with the D value of 0.6739 and the I value of 0.9098. The overlap area of suitable and relatively suitable habitats reached 261.10 hm² and 2048.41 hm², respectively. The overlap area, greatly affected by human activities, was mainly located around the low hills and river valleys in the middle and south of the protected areas. In the future, it is quite necessary to conduct further research on the correlation between the preferences dietary and habits of Rusa unicolor, Budorcas taxicolor, Naemorhedus goral. This will benefit the decision-making and thus result in better-informed and more robust decisions.