In order to understand desert lizard (Phrynocephalus przewalskii) resources as well as protect it well, we used the line intercept method and thirteen environment factors to investigate its habitat selection in Inner Mongolia Helan Mountain National Nature Reserve from May to June and September to October 2017. A total of 92 and 71 utilized plots and 64 and 76 control plots were measured in spring and autumn, respectively. Goodness of fit test, Vanderploeg & Scavia's selection index, Mann-White U test and Stepwise discriminant analysis methods were used to assess fourteen ecological factors in the desert lizard plots and control plots in each season, aiming to determine the main ecological factors affecting desert lizard habitat selection in each season. The results revealed significant differences in desert lizard habitat selection between spring and autumn seasons. In spring, the desert lizard generally selected habitats with adequate sunshine, high surface temperature and low humidity, which ensured its safety by providing rich food resources and cover. Optimum temperature, in particular, was essential for its growth and reproduction. In autumn, the desert lizard preferred meadow areas with rich or moderate food resources and loose soil, ensuring easy access to shelter and food.