Abstract: Land is the resource carrier supporting rural development. The transformation of land use function oriented by sustainable rural development is the necessary requirement to realize sustainable rural land resources utilization. The process of rural development is closely linked to the transformation of land use functions. Based on the survey data of fixed observation points in rural areas of China from 1995 to 2015, this paper quantitatively analyzed the spatio-temporal evolution characteristics and spatial differences of rural land use function transformation in China, and eastern, middle, and western region of China, and discussed the path of sustainable rural development harmonized in China in the future. The results showed that: In terms of time, the social and ecological functions of rural land use decreased from 1995 to 2015, in which the social function was due to the continuous weakening of spatial carrying capacity and employment support, and the environmental function was due to the continuous weakening of environmental purification function. Spatially, the economic, social, and ecological functions of rural land use in eastern and western show obvious spatial differences of advantages and disadvantages. Specifically, employment support and environmental purification in eastern of China, economic output and spatial carrying capacity in central and food supply in western are relatively weak compared with the same spatial functions in other regions. There is a trade-off between economic and social functions, and between economic and ecological functions. There is an intra-group coordination and inter-group trade-off between the two secondary function groups (food supply, economic output, livelihood security and ecological maintenance) and (spatial carrying capacity, employment support and environmental purification). At present, the coupling coordination degree between economic, social and ecological functions of rural land use is mainly in the primary coordination stage and presents a progressive change law from low level to high level coupling. By adopting the multi-functional coordinated transformation and upgrading mode, we can choose the paths of endogenous power and environmental friendliness to comprehensively develop China’s rural areas. Rural regions may be comprehensively developed by selecting multi-functional coordinated transformation and upgrading modes such as endogenous dynamic and environment-friendly.