Based on the supply chain of water resources for the South to North Water Diversion Project, a diversified ecological compensation mechanism that combined the government compensation and the market-oriented compensation was established. By assuming that each member of the water supply chain has the altruistic preference, this paper compared and analyzed the effects of the compensation mechanism of cross-section water quality and the compensation mechanism of water resources protection cost by the central government under altruistic preference. The results show that the water quality, water price and consumer surplus in the water supply chain of water transfer project are positively related to the altruistic preference level of water distributors. The vertical compensation of the central government and the horizontal compensation of the local government can promote the improvement of water quality, and the utility of water receiving areas will increase with the improvement of water quality under altruistic preference. The transfer contract can alleviate the double marginal utility of supply chain members’decision-making under the market-oriented compensation mechanism, alleviate the “hitchhiking” behavior of water distributors, and promote the total utility of supply chain and the welfare of consumers.