ABSTRACT New vaccine research and development (R&D) and production is of importance in combating against prevalent infectious diseases, as vaccines have prevented countless cases of disease and saved millions of lives. We formulate a multi-stage game comprised by one developer, one manufacturer and one government in the new vaccine R&D and production, considering R&D failure risk and capacity sharing. This paper examines the effects of different subsidy forms and two alliance modes. The result reveals that: (1) The government should consistently provide a combo of subsidy to achieve maximum social welfare. The developer has no preference for the form of subsidy in the manufacturer-initiated mode, whereas the manufacturer desires to get subsidised by the per-unit cost form regardless of alliance modes. (2) Being the initiator inside the alliance may not always be the optimal decision for players. The manufacturer should relinquish the role as the initiator if certain requirements are fulfilled. (3) When capacity sharing revenue is substantial or the failure risk is sufficiently low, the government should give priority to using per-unit cost subsidy instead of quality improvement subsidy, and the manufacturer would like to be the follower if per-unit cost subsidy is offered.