Applying the theory of fairness preference to the research on green innovation investment of green supply chain, the income model of green manufacturers and suppliers is established based on the F-S model, and the fair preference for suppliers'green innovation, revenue sharing ratio, fixed subsidy, as well as the impact of the manufacturer's optimal utility under the condition of asymmetric information are analyzed. The results show that under the condition of information asymmetry, fairness preference has no influence on the optimal green innovation investment of suppliers, and does not affect the optimal income sharing ratio provided by green manufacturers, and the subsidies of green suppliers provided by green manufacturers are affected by fairness preferences, and the fixed subsidies given by green manufacturers to suppliers are reduced as the supplier's fairness preference increases, while the green manufacturer's optimal utility is subjected to the fair preference intensity of green suppliers and the combined influence of the strength of their own fairness preferences.