Cooperative R&D has become one of the effective ways for enterprises to improve R&D efficiency and break the bottleneck of R&D resources, but cooperation between enterprises often falls into difficulties due to various factors. Given this, we use the quantum game to study the incentive mechanism of forming cooperative R&D strategic alliances between enterprises, first we establish a stag-hunt game model based on cooperative R&D and independent R&D, then expand the classical strategy to the quantum strategy space, and discuss the strategic characteristics of whether to consider state entanglement, and finally conducts case study to verify the effectiveness of the model. The results show that in the non-entangled scenario or non-quantum scenario, it is difficult to achieve the Pareto optimal result that both sides in full cooperation, because the full-effort one need to bear the risk of betrayal by the on-effort one. However, in the context of maximally entangled quantum game, the risk causing by the defector is borne by himself rather than the cooperator, so both parties will adopt a complete cooperative R&D strategy to achieve a win-win situation. Based on these findings, we establish three incentive mechanisms: information sharing, performance evaluation and responsibility constraint, which provides theoretical guidance for the formation and stability of enterprise cooperative R&D strategic alliance. Furthermore, our research can be extended to other fields, such as the issues of multilateral cooperation between major powers.