In order to sustainably and reasonably evaluate the characteristics and efficiency of regional atmospheric environment, this paper calculated the atmospheric environmental efficiency and regional differences, which is based on the non-radial directional distance function DEA model, among 11 cities in Zhejiang Province from 2006 to 2016 in both static and dynamic dimensions. Compared with existing researches, the atmospheric environmental efficiency evaluation system constructed in this paper not only considered the development of regional economy, but also focused on the air quality output so as to constrain the emission of atmospheric pollutants. The results showed that the average value of the static efficiency of atmospheric environment in Zhejiang was 0.6824 over the past ten years, and there was still about 32 percentage difference from the production frontier. The room for improvement in pollution reduction and control was still huge. The pure technical efficiency was the main factor to impede the improvement of atmospheric environment’s static efficiency in Zhejiang. Meanwhile the dynamic efficiency of atmospheric environment in Zhejiang reached an average annual rate of 7.60%, with a cumulative increase of 93.28%. As well, there were significant urban differences in the growth rate, of which Hangzhou was the fastest, followed by Ningbo and Jiaxing. The improvement of atmospheric environmental efficiency was mainly driven by technological advancement and scale efficiency expansion. The distribution of 11 cities in the four high and low environmental efficiency matrices was relatively uniform, and there was no “Matthew Effect” of H/H or L/L polarization. In the future, Zhejiang needs to formulate corresponding measures to control the atmospheric pollution by fully considering the actual conditions at different cities, and effectively strengthen the environmental management exchanges and collaboration within the province to enhance the overall atmospheric environment efficiency.