In China, industrial pollution has become an urgent problem for policy makers and enterprise managers. To better support industrial development, we need to determine the effectiveness of policies through efficiency evaluation. China’s provincial industrial system consists of two stages: production and emission reduction. The emission reduction stage is composed of three parallel sub stages: solid waste treatment, waste gas treatment and wastewater treatment. In this process, the treatment capacity of industrial wastewater treatment facilities can be used as carry forward variable, which is not only the desirable output of the previous emission reduction stage, but also the input of the current emission reduction stage. Therefore, this paper proposes a dynamic hybrid two-stage data envelopment analysis (DEA) model for eco-efficiency evaluation of industrial systems, and applies it to a case study of Chinese regional industry. Applying the data collected from 2011 to 2015 to the model, the following conclusions can be drawn: (1) During the whole survey period, the average eco-efficiency was 0.9027. The overall eco-inefficiency of China’s provincial industrial system during the study period is mainly due to low efficiency of solid waste treatment and waste gas treatment. (2) The average eco-efficiency of provincial industrial system increased steadily from 2011 (0.6448) to 2014 (0.6777), but decreased slightly in 2015 (0.5908). (3) The carry forward treatment capacity of industrial wastewater treatment facilities has a remarkable impact on provincial industrial system efficiency scores, especially at the wastewater treatment stage (0.6002 vs 0.3691). (4) Provincial industrial system exists distinct geographical characteristics of low efficiency. This study has important guiding significance for policy makers and enterprise managers who are concerned about industrial pollution control.