Abstract: Rural territorial multifunction is essential to the sustainable development of a rural system. It is an important way to effectively identify the spatial pattern and obstacle functions in a rural territorial system, in order to optimize the allocation of rural elements and promote the rural revitalization. In theory, the effective identification of multifunction can provide scientific reference for the regional development orientation, spatial division, and mechanism innovation of rural revitalization. In practice, a useful guideline can be available for the functional orientation of rural areas, development plans, implementation of rural management policies and transformation. Taking Shandong Province as a research object, this paper aims to analyze the interaction between elements, structure and function in the rural regional system. According to the aspects of living, production, and ecology, six sub-functions were divided, including living and inhabitancy, life security, agricultural production, non-agricultural production, ecological conservation, and environmental maintenance. Firstly, a multifunction evaluation index system was established to calculate the indicator of rural territorial multifunction, together with the internal operation mechanism of structure and elements in the rural man-earth areal system. Secondly, an OpenGeoda software was selected to evaluate the multifunction global spatial autocorrelation of rural areas, and then an ArcGIS10.3 hotspot analysis tool was used to identify the local spatial autocorrelation. Finally, the control measures were proposed after a spatial partition type was constructed, where an obstacle function was used to clarify the obstacle diagnosis model, according to the multifunctional integration and coordination degree of rural areas. The results show: 1) The mean values of rural living function, production function and ecological function in Shandong Province were 0.429 8, 0.463 5, and 0.574 2, respectively. The comprehensiveness and coordination were between 0.28-0.76 and 0.51-0.99, indicating the spatial characteristics of "weak living function, medium production function and strong ecological function"; 2) The multifunctional Moran's I index in rural territorial system was all higher than 0.4 in Shandong Province. The spatial distribution features were positively correlated, particularly concentrated on the low functional values. Three regions, from the hot spot area to the cold spot area, the transition from Jiaodong Peninsula to central Shandong, and west Shandong, were in the form of spot patch, encircling strip block, segmented surface, and irregular mosaic surface, respectively; 3) According to the coupling relationship between comprehensive and coordination degrees, the rural territorial system was divided into five zones, including priority promotion area, key promotion area, potential promotion area, collaborative optimization area, and moderate optimization area. However, the obstacle function of each region has the double attribute of identity and difference. Specifically, the living function of population was the common obstacle of each region, whereas, the obstacle degree varied in non-agricultural production function and environmental maintenance function; 4) Some suggestions can be gained during this time. The regulation and control of rural territorial multifunction in Shandong Province can take "double high" as the goal, according to the policy of "finding the short board and developing together", while strengthen the local key promotion and the optimization of rural functional areas based on local conditions, thereby to provide a promising potential to the rural high-quality development in the new era.