This paper constructs a game model of the alliance’s cooperative R&D to study how to reduce the alliance members’ moral hazard of and increase their investment through choosing the right alliance structure and the way of profit-sharing, in order to promote the success of cooperative R&D activity. This research has shown: in different alliance structures and profit-sharing ways, the alliance members’ investment is gradually increasing as the market return rate increases; in different alliances, the R&D investment under distributing according to the investment proportion is higher than average distribution; in different profit-sharing ways, gathered R&D alliance’s investment is higher than parallel R&D alliance’s.