To identify the main environmental factor that plays a key role in habitat selection of rodents in the western slope of Helan Mountains, and to explore how the interaction among rodent species affect habitat selection, we selected geographic factors (altitude, gradient, slope direction), vegetation factors (vegetation coverage, vegetation height, height of shrubs/arbors) and other factors (distance from the water, away from the road distance, distance from shrubs/arbors) to analyze the habitat selection and interspecific relationship of rodents by resource selection function model and logistic regression models. The results showed that there were significant differences in the habitat selection among six captured rodent species. Apodemus peninsulae preferred high-altitude habitats covered with dense shrubs/arbors. Meriones meridianus preferred sparsely vegetated semi-desert habitats at lower altitude, and did not avoid the road and human disturbance. Cricetulus migratorius preferred habitats which were far away from water, covered with dense shrubs/arbors and close to roads. Spermophilus alaschanicus preferred the low-altitude habitats where are rich in vegetation. Cricetulus eversmanni preferred the high altitude habitats close to roads. Niviventer niviventer preferred habitats with higher altitudes, higher slopes and far from water. The relationship between rodent species is mainly avoidance or random. Our study is contributing to understand the changes of rodent distribution and population dynamics. It can provide basic data and scientific basis for protecting biological resources, predicting and forecasting rodents damage, and comprehensive management of the regional damage that caused by rodent in Helan Mountains.