This paper investigate the effect of various subsidy Schemes on Cournot duopoly with R&D behaviors. Firms invest in 1st stage to reduce marginal cost and Compete noncooperatively in 2nd stage. Without subsidy, R&D cooperation is more desirable than R&D competitpn in the presence of sufficient R&D spillover. Subsidy scheme that subsidies proportional to quantity and propotional to R&D expenditure is not desirable. But Subsidy scheme that subsudies propotional to square of quantity and propotioal to R&D expenditure is desirable. If firms compete in 1st stage, Regulator can accomplish social optimum with less subsidy than that in the R&D cooperation. But more Information is required for regulator to accomplish social optimum in the R&D competition.