Facing the uncertainty of internal and external environment, how to reasonably manage the cash flow and improve the competitiveness has become a hot research topic. Based on the theory of financing priority, liquidity preference and financing constraint, this paper analyzes the relationship between cash flow uncertainty and enterprise innovation, and verifies the effect of cash flow uncertainty on enterprise innovation. In addition, government subsidies and senior management shareholding are added into the original model as moderating variables to explore whether external factors of enterprises such as government subsidies and internal factors of enterprises such as governance structure will have an impact on the relationship between cash flow uncertainty and enterprise innovation.