According to "Guidelines on the Establishing a System of Nature Reserves Dominated by National Parks", zoning control is required to implement in national parks to achieve the objective of most strict protection. However, what factors could be used in zoning is debated. For finding out a set of index system for zoning, we study the Qianjiangyuan National Park System Pilot Area (hereinafter referred to as Qianjiangyuan National Park) as an example. We collected the multi-source data including the general environmental information (such as Digital Elevation Model, DEM; Normalized Difference Vegetation Index, NDVI; impacts of traffic and permanent basic farmlands), major distribution of wildlife (such as wild animal and botany vegetation;Habitat suitability of Muntiacus crinifrons and Syrmaticus ellioti), natural resources protection (such as Gutianshan National Natural Reserve; Qianjiangyuan National Forest Park; Qianjiangyuan Scenic Spot and Ecological public forests) and ecological status indicators (such as evaluation of ecological function suitability; evaluation of natural resources carrying capacity; red lines of three spatial zones and land use planning), and used analytic hierarchy process (AHP) to build a set of index system for zoning. Based on the results of AHP, we adopt the spatial overlay analysis technique to obtain the spatial distribution including the core protected zone and general controlled zone in Qianjiangyuan National Park, and then compared our results with the current functional zones. The results showed that:(1) the analysis based on the multi-source data can effectively recognize high ecological protection value in Qianjiangyuan National Park; (2) compared to the actual functional zones, the overlap areas of these two results is 197.70 km², which indicated that the total accuracy of spatial analysis was 78.07%, and the overlap areas in core protected area and general controlled area were 127.99 km² and 69.71 km², which meaning that the accuracy in core protected area or general controlled area were 83.55% or 69.67%, respectively; (3) the reasons that affect the accuracy between spatial overlay analysis and the actual functional zones are including that insufficient basic data in the new areas, and errors introduced by qualitative analysis for solving the fragmentation of the zoning. Overall, this study confirmed that the multi-source spatial data analysis technology could efficiently and accurately work on zoning core protected area or general controlled area of national parks, and could be replicated into other nature protected areas, but it still needs more basic data or optimize algorithm to improve zoning accuracy.