Innovation ability has become one of the core elements in the pursuit of China’s green growth, and high-tech industries are playing a leading role in technological innovation in China. With the rapid development of China’s high-tech industries, their innovation efficiency has attracted widespread attention. This article aims to illustrate a shared inputs two-stage network Data Envelopment Analysis (DEA), to measure the innovation efficiency of high-tech industries in China’s 29 provinces from 1999 to 2018. The results indicate that there are obvious differences in the innovation efficiency of the provinces. The technology development efficiency, the technical transformation efficiency, and the overall innovation efficiency of the developed east coast provinces are generally higher than those of the backward central and western provinces. This article further applies the spatial econometrics model to analyze the factors influencing the innovation efficiency of high-tech industries. We have found that government support, R&D input intensity, industries aggregation, economic extroversion, and the level of development of the modern service industries cause varying degrees of impact on innovation efficiency.