Under the economic recession, it is an inevitable choice to emphasize the forward shift of firms’ R&D investment stage and to strengthen the investment in basic research and applied research for high-quality development. This paper incorporates the transmission process from external risk perception to enterprise internal risk perception into the analysis of enterprise R&D investment decisions under economic policy uncertainty, and reveals the mechanism affecting the enterprise′s R&D investment decisions in different stage from the supply of resources effect and the opportunity cost effect. Based on listed manufacturing firms from 2011 to 2020, this paper founds that:1) When the opportunity cost effect dominates, economic policy uncertainty has significantly positive impacts on firms′ research stage, and when the resource supply effect is dominant, there is a significant inhibitory effect of economic policy uncertainty on the development stage; 2) Mechanism tests shows that economic policy uncertainty enhances the bank′s short-term credit preference, which strengthens firms′ own risk perception and hedge risks with cash flow and short-term debt, thereby effectively mitigating the negative impact of short-term credit on research investment. This effect turns out to be stronger in firms with mature enterprise, low financing constraints and low reliance on short-term borrowing. Meanwhile, economic policy uncertainty reduces stock liquidity, thereby effectively inhibiting firms′ development investment. This paper emphasizes the mechanism by which economic policy uncertainty is first perceived by financial institutions and capital market, and then transmitted to firms through external financing constraints, reinforcing firms′ own risk perceptions and employing risk hedging tools to regulate R&D investment at different stages.