Abstract: Customers’ preference to greener agricultural products makes farmers and downstream manufacturers realize the importance of improving the greenness of primary agricultural products. Aiming at the farmers and risk-averse manufacturers’ decision on green investment in primary agricultural products, the payoff matrix is obtained by developing a Stackelberg game. Based on evolution game theory, the evolutionary process of the two heterogeneous groups has been analyzed and the ESS (Evolutionary Stability Strategy) gained. A simulation of the system evolutionary process has also been conducted. The results show that facing the customers who possess green purchase preference, at least one side of the farmers and manufacturers will invest in improving the greenness of primary agricultural products. When they collaborate and share the investment costs, an ideal equilibrium state system will be evolved; under the ideal equilibrium state, the evolutionary velocities and revenue (utility) of the farmers and manufacturers are directly related with the manufacturers’ risk-averse parameters and costs sharing proportion.