This paper integrates the R&D-based model with environmental protection, and sets the intermediate goods sectors as monopolistically competitive and as polluting industries. The government sector has two policies. One policy is to tax polluters, the intermediate goods sectors, for their pollution inputs to finance pollution prevention. The other policy is to impose a lump-sum tax on households to partially finance the subsidy expenditure for the R&D sector. This paper discusses how the two policies affect the economic growth rate and welfare. By comparative-static and numerical simulation analysis, we find that taxing polluters to finance pollution prevention will improve environmental quality. Moreover, there exists an ”optimum pollution tax rate for economic growth” and an ”optimum pollution tax rate for welfare” to maximize the economic growth rate and welfare, respectively. On the other hand, raising the R&D subsidy rate is helpful for increasing the economic growth rate. Furthermore, there exists an optimum R&D subsidy rate to maximize welfare.