A game theory approach is used to discuss the cooperative RD programs between the manufacturer and supplier in a supply chain. Under the condition of two non-cooperative games and cooperation, this study is to analyze the differences of RD investment, co-op reimbursement policy, and profit between the manufacturer and supplier in the entire system. The results demonstrate that the collaborative cooperation can form win-win situation. Nash bargaining approach and utility theory were used in the Pareto efficient scheme to determine the best cooperative program.