This paper selects 573 technology-based enterprises on the Science and Technology Innovation Board, and selects corporate finance, government-guided fund investment, macroeconomic and other data from 2011 to 2021. By using fixed effect model and multi-period DID model, this paper not only analyzes the intermediary effect of financing constraints, but also compares the effect of the two modes of fiscal cooperation on the innovation output of enterprises in different growth periods and in different regions. The results show that the credit model and investment model of fiscal cooperative finance promote the innovation output of enterprises by easing financing constraints. The investment model has better effect on promoting the innovation of enterprises in the early stage of growth, and the credit model has better effect on promoting the innovation of enterprises in the stable stage of growth. Both the investment model and the credit model significantly promote the innovation of enterprises in the eastern region. The central region depends more on the investment model, while the western region depends more on the credit model. On the one hand, improve the mutual cooperation between the two modes of fiscal coordination and finance, on the other hand, the western region should develop and improve the scientific and technological financial service system, and enhance the promotion role of investment mode.