China's new urbanization process requires coordinated development between cities and rural areas. Territorial functions of rural areas are defined as advantageous effects on nature and human society that, in particular, rural systems perform via their property and interactions with other systems at certain social development stages. This paper establishes an index system for evaluating rural territorial functions including agricultural function, social function, economic function and ecological function. By establishing a model based on a General Regression Neural Network (GRNN) with the county-level as the basic unit, we comprehensively evaluate the rural territorial functions of 109 counties and/or cities in Henan province, China in 2000, 2005 and 2010. Results show that compared with that in 2000, each function in 2010 improved, with the spatial heterogeneity of economic function the most evident, social service function comparatively balanced and spatial distribution of agricultural production function changing little. Cluster analysis was adopted to study the major functions of rural regions. Henan was divided into six major function zones to enhance administrative management and developmental policy. The six major function zones are Type I (core economic development zone), Type II (agricultural production safeguarding zone), Type III (function improving zone for rural areas), Type IV (model zone of livelihood and social services), Type V (economic restructuring and development zone), and Type VI (nature conservation areas). Different development goals and development strategies should be considered according to different major function areas to achieve the coordinated development of urban and rural areas in China.