In order to study the spatial disequilibrium characteristics of innovation efficiency level of China's high‐tech industry, this paper uses the stochastic frontier model to measure the innovation efficiency of China's high‐tech industry and the Mookherjee & Shorrocks Gini coefficient decomposition method to measure the spatial disequilibrium characteristics of the innovation efficiency level of China's high‐tech industries. The data on the development of high‐tech industries in 29 provinces (municipalities directly under the Central Government and autonomous regions) in Mainland China from 2000 to 2017 are selected as research samples. Results show that: first, the distribution map of the average innovation efficiency level of high‐tech industries drawn by GIS intuitively shows that the spatial distribution of innovation efficiency level of China's high‐tech industries, it is manifested in the gradient distribution of low innovation efficiency in central and western regions and high innovation efficiency in eastern regions. Second, the Gini coefficient calculation and its decomposition results show that the overall relative differences in the innovation efficiency level of China's high‐tech industries show a slight downward trend, and the gap between regions is the main source of the overall gap.