China’s social and economic development is in a critical period of transition. With the implementation of the Rural Revitalization Strategy, new rural industries and new formats have developed rapidly. Profound changes have taken place in the human–land relationship, population structure, industrial structure, and rural functions in the vast rural areas, which have a huge impact on the function and value of rural homesteads. The functional evolution of rural homesteads has a strong driving effect on the change of function value of the homestead. The functional value of rural homesteads is affected by the social and economic development conditions, location, resource endowment, land use policy, rural land trading market, the development of new industries and new formats, and the evolution of homestead function; different homestead functions have different values, especially in the non-agricultural production function and asset function of the homestead. To revitalize the idle and inefficient use of the homestead and fully manifest its value when the homestead is transferred or withdrawn, it is necessary to scientifically calculate the homestead value according to the principle of “what function is lost and what value is compensated”. This paper adopts basic geographic data, rural land transaction data, and social and economic data, and it uses participatory rural appraisal, the land estimation method, and the comparative analysis method. According to the classic theory of “structure determines function and function determines value” in systems engineering, the equivalent substitution method and market value method are used to measure and compare the functional values of traditional agricultural villages and tourist homestay villages before and after the functional evolution. The results show that (1) the leading functional evolution of homestead landlords is closely related to the level of social and economic development. The change in the functional value of the homestead presents the same law as the evolution of its leading function. (2) The functional evolution of the homestead has a strong driving effect on its value change. The increase in value caused by the functional evolution of homesteads in homestay villages is significantly higher than that in traditional agricultural villages. (3) The functional value of the homestead is affected by the social economy, location, resource endowment, land use policy, rural land trading market, business development, and the functional evolution of the homestead. (4) It is suggested that the state formulates the compensation standard for voluntary and paid withdrawal of homesteads according to the “functional value theory of homesteads”, to reduce the unfair value compensation caused by location differences.