In the process of urban-rural Integration, the reform of the “separation of three rights” of homesteads has released huge institutional dividends for the vigorous utilization of rural homesteads. With the gradual deepening of the reform of the homestead system the number of disputes related to the transfer of the land use of rural homesteads is increasing rapidly. Based on the quasi-case research method, this paper integrates the relevant case facts, the focus of the dispute, the legal basis, and other case elements and realizes the judgment of case similarity based on the legal argument model, which aims to solve the problem of realizing justice in the distribution of land value-added benefit in homestead disputes. It also puts forward the realization mechanism reform suggestions based on the perspective of judicial governance, so as to demonstrate the ways in which conflicts arise and are resolved in the distribution of value-added benefit in China’s rural homestead transfer system. By using the search tool of the “China Judgment Document Network” to screen a total of 305 valid samples, it was revealed that the core problem of China’s homestead governance is the unfair distribution of land value-added benefit; that is, it is difficult to achieve effective distribution of land value-added benefit among farmers, collectives, and governments. The core litigation points in rural homestead disputes include homestead policies and the application of law, the litigability of cases, the scope of the subject, and the realization of powers, as well as the quantitative basis and rule scheme. From the perspective of judicial governance, the deep-seated issues in the distribution of value-added benefits reflected in the points of dispute are examined as follows: (1) the subject of the dispute faces judicial avoidance; (2) There is a game relationship in the value of subject rights; (3) it is difficult to quantitatively adjudicate under the existing allocation rules; (4) Institutional difficulties such as insufficient eligibility of applicable policies. Based on the conclusions of the above problems, this study proposes a judicial governance path for the realization of homestead value-added benefit distribution justice: the governance model is reorganized and optimized based on the purpose of realizing distributive justice; the value of rights throughout the process is integrated based on initial acquisition and redistribution; a multi-center linkage governance mechanism is constructed based on the coordination of homestead value-added benefit through all stages, which is supposed to provide an important reference for the judicial governance path for developing countries with similar difficulties, including China, to achieve justice in the distribution of land value-added benefit.