Understanding the impacts of environmental factors on spatial–temporal and large-scale rodent distribution is important for rodent damage prevention. Investigating rat hole density (RHD) is one of the most effective methods to obtain the intensity of rodent damage. However, most of the previous field surveys or UAV-based remote sensing methods can only evaluate small-scale RHD and its influencing factors. However, these studies did not consider large-scale temporal and spatial heterogeneity. Therefore, we collected small-scale and in situ measurement records of RHD on the northern slope of the Tien Shan Mountains in Xinjiang (NTXJ), China, from 1982 to 2015, and then used correlation analysis and Bayesian network (BN) to analyze the environmental impacts on large-scale RHD with satellite remote sensing data such as the GIMMS NDVI product. The results show that the built BN can better quantify causality in the environmental mechanism modeling of RHD. The NDVI and LAI data from satellite remote sensing are important to the spatial–temporal RHD distribution and the mapping in the future. In regions with an elevation higher than 600 m (UPR) and lower than 600 m (LWR) of NTXJ, there are significant differences in the driving mechanism patterns of RHD, which are dependent on the elevation variation. In LWR, vegetation conditions have a weaker impact on RHD than UPR. It is possibly due to the Artemisia eaten by the dominant species Lagurus luteus (LL) in UPR being more sensitive to precipitation and temperature if compared with the Haloxylon ammodendron eaten by the Rhombomys opimus (RO) in LWR. In LWR, grazing intensity is more strongly and positively correlated to RHD than UPR, possibly due to both winter grazing and RO dependency on vegetation distribution; moreover, in UPR, sheep do not feed Artemisia as the main food, and the total vegetation is sufficient for sheep and LL to coexist. Under the different conditions of water availability of LWR and UPR, grazing may affect the ratio of aboveground and underground biomass by photosynthate allocation, thereby affecting the distribution of RHD. In extremely dry years, the RHD of LWR and UPR may have an indirect interactive relation due to changes in grazing systems.