Abstract: The high-tech enterprise is an important subject for promoting new industrialization at a high level in the new era, and a main driver of new quality productive forces. The production efficiency and innovation level of high-tech enterprises is an important issue of concern to scholars. Using the microscopic data of enterprises in the national high-tech zone from 2013 to 2019, we construct the non-parametric production function model. The assumption that production factors have a linear impact on output is relaxed, and the endogenous problems that may exist when high-tech enterprises make decisions on the input of production factors are considered. The production function of high-tech enterprises is estimated by using the two-stage nonparametric method. The productivity at the enterprise level is calculated and analyzed. The result shows that the total factor productivity of start-up high-tech enterprises is low, which means the improvement of total output is still in the early stage of factor accumulation and mainly dependent on the input of various production factors. What’s more, the total output is more sensitive to the input of capital factors. There is heterogeneity in the productivity of enterprises in different technical fields. The productivity of manufacturing export enterprises is significantly higher than that of non-export enterprises, and the type of foreign trade has no significant impact on service-oriented enterprises. This paper provides policy recommendations for the government to promote the development of high-tech enterprises in China.