“Same location with equal rights and equal price” is an ultimate goal of building a unified urban and rural construction land market. However, for a long time, the cognitive limitations of rural homestead use right, circulation obstacles, and the difficulty in forming a rural homestead market make it difficult to realize the value of rural homestead. There is a big deviation between the actual transfer price and the functional value of rural homestead, and there exists also a huge gap between rural homestead and urban homestead. Therefore, this study selected 287 cases of rural homestead and 534 cases of urban homestead in Beijing and built a measurement framework of segmented deviation of multiple values of rural homestead use right. The study used a multi-function model and deep belief network (DBN) to measure the “three-dimensional value” and “two-level deviation” of the actual transfer price, the functional value, and the urban-rural equal right value. The results show that: (1) The average difference between the functional value and actual transfer price of rural homestead use right in Beijing is 8748.08 yuan/m2, and the average value deviation is 63.14%, showing the spatial distribution characteristics of zonal decline, which may be caused by the cognitive deviation of the functions of rural homestead and citizenship rights, the comprehensive influence of supply-demand matching degree, market integrity, policy externality and other factors; (2) The average difference between the equal right value and functional value of rural homestead use right is 27192.81 yuan/m2, the average deviation is 68.32%, showing a significant spatial distribution feature of central diffusion, which may be caused by the differences in the integrity, clarity, and stability between urban and rural homestead use rights. Based on these results, this article proposed that in the future, the manifestation and realization of value of rural homestead should be carried out in two steps: First, improve the “rural secondary market” of rural homestead, gradually correct farmers’ cognition of the functions of rural homestead use right and the manifestation of qualification right; Second, according to urban property situation, build a “unified urban-rural market” by constantly improving the functions, promoting the further manifestation of the complete value of rural homestead, then realize the goal of “same location with equal rights and equal price” for a relatively coordinated unified urban and rural construction land market.