Based on stochastic frontier model of trans-log production function, this paper makes an estimation on the capital-labor substitution elasticity of industrial sectors in China from 2001 to 2015 and an analysis on the influencing factors. The results show that: the capital-labor substitution elasticity of most industries in the labor-intensive industry group is greater than that in technology-intensive industry group, while the latter is greater than that in capital-intensive industry group. The openness, R&D intensity, nature of property right, capital-labor ratio, debt to assets ratio of the industries, the implementation of Labor Contract Law and the financial crisis can all influence the capital-labor substitution elasticity.