Ecological environment governance of water resources is the foundation and key measures to ensure good water quality in China's South-to-North Water Transfer Project. However, as a limited rational economic person, considering their economic benefit, different involvers in China's South-to-North Water Transfer Project show different types of preference relations and make different action decisions as well as play conflicts with each other, which have a negative effect on ecological environmental governance. To overcome above-described shortcomings, heterogeneous preferences are integrated into graph model for conflict resolution (GMCR) to resolve ecological environment governance conflict of water resources. Specifically, first, four different structures of preference expression, including preference orderings, utility functions, multiplicative preferences, and additive preferences, are used to represent decision-maker's (DM's) preference information over states. Then, a novel preference ranking method is designed to calculate the ordinal preferences over all states by using matrix representation. Based on this, a set of heterogeneous stability definitions is proposed in GMCR to describe human diversified choice and behavior in detail, and it is applied to the ecological environment governance conflict of water resources in China's South-to-North Water Transfer Project. The heterogeneous stability analysis result showed that incentive policies used by water resources agencies can effectively encourage local governments and enterprises to actively participate in the ecological environment governance, and promote the ecological environment governance conflict to evolve into a state of equilibrium.