Implementing the collective ownership of homestead is an objective need to build up the basis of the rural collective economy, which conforms to the basic logic that the reform of rural property right system must adhere to the bottom line of collective ownership. From the perspective of the Civil Code, this article explains the policy logic of implementing collective ownership of homesteads, analyzes the practical difficulties in the process of practice, and explores the practical path of implementing collective ownership of homesteads under the “separation of three rights”. Results show that the implementation of collective ownership of homestead is of great practical value for consolidating the dominant position of collective economic organizations, safeguarding farmers’ property rights and realizing rural common prosperity. However, due to multiple factors such as the virtual exercise of collective ownership by farmers, the complex and diverse interests of homestead owners, and the “closure” of homestead use rights, the implementation of collective ownership of homestead also faces many difficulties and challenges. The academic community needs to strengthen research on the practice of the rule of law, to place the study of collective ownership of homesteads under the logic of national legal construction, and to form a positive interactive relationship between academic research and legal construction. Therefore, this paper recommends combining the relevant provisions of the Civil Code and focusing on the main line of handling the relationship between farmers and land, exploring the implementation path of collective ownership of rural homesteads from clarifying the main body of collective ownership of homesteads, strengthening collective ownership rights, and establishing a new model of homestead management.