Insufficient protective investment in farmland (PIF) leads to degraded land resources and inefficient agricultural operations, which have always been one of the main problems that plague developing countries. Most researches have focused on the impact of objective arrangements of property rights on farmers’ PIF, and lack of discussion on farmers’ cognition of property rights. Based on a data of 8 provinces, and applying the Expectation theory and the “Tragedy of the Commons” theory, this paper examined the influences of the cognition of land ownership (CLO) on farmer’s PIF by the Tobit model and the Probit model. Results show that: The PIF of the investigated farmers is not satisfactory that they use only 1.442 tons manure per hectare and only 12.1% of the plots were taken engineering measures, including leveling land, constructing terraced land, and building irrigation systems from 2009 to 2012. farmers’ CLO can be divided into strong CLO and weak CLO. Firstly, the CLO has a significant positive impact on the application amount of manure. On average, farmers with strong CLO applied 1.137 tons more manure per hectare than that of farmers with weak CLO. Secondly, the CLO has a significant and robust impact on engineering measures. Strong CLO promotes engineering measures. Farmers with strong CLO have 4.9% higher probability of conducting this series of PIF than that of farmers with weak CLO. Therefore, under the background of “system first, cognition lag”, further clarification of property rights and strengthening farmers’ CLO are of great significance to promoting farmers’ PIF.