Encouraging enterprises to expand R&D investment is highly significant for enhancing national innovation capabilities. It utilized the data from the Chinese employer-employee matching survey to investigate the impact of flexible employment mode on the R&D investment intensity of enterprises from the perspective of employment pattern. The findings are as follows： the flexible employment model has an inhibitory effect on the R&D investment intensity of enterprises； from the perspective of labor factor allocation， the decline in the level of human capital in enterprises is an important mechanism that suppresses the R&D investment intensity of enterprises by adopting flexible employment mode； expanding the scale of enterprises and enhancing the labor protection effect of enterprise trade unions weaken the inhibitory effect of flexible employment mode on the R&D investment intensity of enterprises.The findings not only help to deepen the understanding of the relationship between employment pattern and corporate innovation， but also provide empirical references for the decision-making theory of innovative R&D investment as well as for optimizing the implementation path of the innovation-driven development strategy.