To promote high-quality economic development, it is essential to optimize the financing structure, build a robust capital market, fully leverage the operational mechanisms of the capital market, mobilize financial resources that are inefficiently utilized, and facilitate financing channels for the real economy. Accordingly, China’s capital market has undergone the reform of its issuance system, gradually implementing a stock issuance registration system. A review of the literature on the registration system reveals that most scholars have focused their research on the efficiency of the capital market, with little attention paid to its impact on the total factor productivity of enterprises. This paper employs the PSM-DID model as its research methodology to investigate whether the reform of the capital market registration system can affect the total factor productivity of listed companies, providing empirical evidence that supports the foundational institutional construction of the capital market to facilitate the high-quality development of the real economy. The results indicate that implementing the capital market registration system can enhance the total factor productivity of enterprises. This conclusion remains valid even after conducting robustness checks using various methods to measure enterprise TFP, adding industry fixed effects, and re-selecting the data. The mechanism analysis shows that the implementation of the registration system affects the total factor productivity of enterprises mainly by easing the financing constraints of enterprises and promoting the R&D innovation of enterprises. The further heterogeneity test shows that the implementation of the registration system has a more significant promoting effect on the total factor productivity of non-state-owned enterprises and enterprises with high industrial competition. Compared with previous literature, this paper may have the following marginal contributions: first, it provides an important reference for the discussion of the advantages and disadvantages of the full implementation of the registration system and opens up a new research direction for the registration system research; second, it enriches the relevant literature on the factors affecting the total factor productivity of enterprises to extend its research space; third, it provides policy inspiration for deepening financial reform and improving the efficiency of financial resource allocation. The research of this paper reveals the inner logic and mechanism of the service efficiency of the capital market to the real economy to some extent. To give full play to the service efficiency of the capital market and improve the total factor productivity of enterprises, it is necessary to continue to promote the deepening and strengthening of the stock issuance registration system, promote the virtuous cycle development of the capital market, optimize the efficiency of factor resource allocation, and encourage pragmatic innovation of enterprises.