Abstract: The system of three rights separation is regarded as another important farmland property right system reform after the household contract responsibility system, which is of great significance to the development of forestry. Based on the analysis framework of “structure-action”, this paper takes Xixia Village as an example to study the influence of the three rights separation system on the transformation of forestry organizational management model. The results show that: ① the defect of informal three-right separation system is the reverse incentive of the evolution of forestry organizational management model; ② the formal three-right separation system has an incentive and restriction effect on the evolution of forestry organizational management model through transaction costs and security psychology; ③ at the governance level, the institutional arrangement of property rights within the organization has an incentive and restrictive effect on the evolution of the forestry organizational management model through power and power incentives, forest farmers’ benefits, opportunity costs and transaction costs; ④ at the level of resources allocation, the circulation of management right has an incentive and restrictive effect on the evolution of forestry organizational management model through economic performance and operating cost. In view of the restrictive function of the three rights separation system, corresponding suggestions are put forward.