The process of urbanization in China has been accompanied by the conflict of land expropriation, which is not conducive to social stability. Different from the previous angles and methods of studying the conflict of agricultural land expropriation, this study puts forward a new behavioral perspective on the basis of game theory, and constructs an evolutionary game model of the conflict of agricultural land expropriation in China from the perspective of multi-dimensional preference. It also discusses the impact of different preference combinations on the conflict input, net income and utility of various stakeholders in agricultural land expropriation. The results show that under the influence of complete self-interest preference, the degree of protection of farmers’ land rights and interests affects the probability of conflicts in compensation for agricultural land expropriation. However, under the influence of multi-dimensional preference combination, agricultural land expropriation can be carried out smoothly only when the reciprocal altruism preference of local government and farmers is strong and the loss aversion preference is weak. These insights have implications for the sustainable development of land, including government involvement and farmers participation, particularly in the context of developing countries.