Currently, global food security is very unstable and risky. An important link to ensure food security is agriculture. However, there is a general tendency to financialization in entities. This article examines the possibility of the impact of financialization on food security from the micro-perspective of enterprise innovation. Taking China, a populous and developing country, as an example, the operating data of the listed agricultural companies of Shenzhou-Shanghai shares A from 2010 to 2020 were selected as research samples to test the impact of financialization on the innovation of agricultural enterprises, expand relevant theories, and further analyze the heterogeneity of agricultural companies. The results show that: firstly, there is a trend of financialization in Chinese agricultural enterprises and there is a significant U-shaped relationship between financialization and the input of agricultural enterprises. If the degree of financialization is too high, it will have a negative effect on agricultural enterprises and impact on food security. Second, there is firm heterogeneity in the innovation input of agricultural enterprises caused by financialization. Excessive financialization is more obvious in the "crowding out" of innovation input from state-owned enterprises large-scale enterprises and agricultural manufacturing enterprises, indicating that excessive financialization has a greater impact on food security of these three types of agricultural enterprises. Final, this document presents corresponding policy suggestions for the financial development of Chinese agricultural enterprises to promote agricultural innovation and ensure food security.