Multifunctional zoning is the primary basis for developing differentiated spatial planning systems and management policies of territorial spaces. The purpose of the paper is to generate an integrated multifunctional zoning scheme of the territorial space in Panxi by employing the functional significance assessment funded on the niche theory and its measurement models, in order to benefit the high efficiency land utilization and other socioeconomic development initiatives, such as the industrial poverty alleviation and mountainous urbanization in the regional scale. In this paper, the six main functions of territorial space were selected and the corresponding index systems were established for the Panxi Area. First, the significances of six territorial functions were evaluated using two niche models. Second, the K-means clustering method was employed to cluster the functional significance grades, acquiring the integrated multifunctional zoning scheme after qualitative adjustment. The results showed that the spatial distribution characteristics of the functional significance for territorial spaces were different. Prominent regions with higher functional significance of agricultural production were concentrated in the vicinity of the Anning River Basin. The distributions of higher significance for industrial development and mineral resources supply functions were correlated with the overall economic development in the Panxi Area. The regions with higher functional significance for tourism & leisure showed advantages on tourist attractions’ quality. The regions with higher significance for habitat service and ecosystem services functions presented advantages on good livability and ecological conditions. The integrated multifunctional zoning scheme for territorial space was highly in consistence with the Major Function Oriented Zoning of Sichuan Province and the “Thirteen Five” Development Plan for Panxi Economic Zone. Generally, the results indicated the rationality and feasibility of the research method, which provides a theoretical basis for coordinating and shaping the structure and pattern of territorial spaces, especially in the mountainous environment with distinct geographical as well as functional differences.