Three Rights Separation is a major institution innovation of China's rural land property rights system, targeted to promote the optimal allocation of resources through the refinement and clarification of property rights of agricultural land, encouraging property rights transfer and optimization, finally enhancing agriculture development and transition. However, it remains untested whether the separation of three rights can improve farmers' long-term expectations of the safety and security of property rights, and subsequently change their behaviors. Based on the mechanism of "policy reform-policy cognition-behavior change" and a case study of Qingpu district, where the practice of land property rights transfers was started early, the policy cognition and behavior changes of the new agricultural entities was studied. Questionnaire investigation and semi-structured interviews were carried out for data collection and structural equation model was applied to study the influence of policy cognition on their behavior changes to enlarging scales, enhancing long-term investment and shifting to environmentally friendly agriculture. It is found out that the policy cognition is of positive impacts on their behavior changes and subsequently contributes to the transformation of agriculture; the better cognition also leads to greater behavior changes. Thus more attention should be paid to enhancing the supporting system of the Three Rights Separation Reform, strengthening policy transparency and interpretation to farmers, improving the human capital stock of agriculture, in order to provide strong endogenous power for the transformation and upgrading of agriculture.