Considering the manufacturer's fairness neutrality and fairness preference, the influence of the manufacturer's fairness preference and corporate social responsibility (CSR) level on the decision and benefits of the green supply chain is studied. The results show that: 1) The manufacturer's fairness preference behavior not only helps lower the wholesale price and retail price, but also helps improve the product green degree, market demand and retailer's profit. However, it does harm to the manufacturer's profit to some extent. The direction that the overall profit of the supply chain changes with the manufacturer's fairness preference is related to the level of his CSR; 2) The higher the manufacturer's share of the supply chain CSR, the lower the wholesale price and manufacturer's profit will be, while the retailer's profit will be higher. Nevertheless, the effects of the manufacturer's CSR allocation on the retail price, product green degree, market demand and system's profit vary with the degree of the manufacturer's fairness preference; 3) A higher degree of the manufacturer's fairness preference and his CSR allocation are not necessarily better for the green supply chain. The reasonable fairness preference and CSR level of the manufacturer not only contribute to the improvement of the product green degree and profit of the green supply chain, but also to realizing the optimization of consumer surplus and social welfare.