With the deepening of urbanization and industrialization, as well as the exacerbation of energy consumption, China is facing a severe situation in which nitrogen oxide (NOx) emissions reduction is imperative. In this study, it is aimed to put forward countermeasures and suggestions to reduce NOx emissions by analyzing the impact and mechanism of new urbanization, the agglomeration of energy-intensive industries and mutual interactions on China’s NOx emissions. By analyzing the data of 30 provinces in China from 2006 to 2017, this paper adopted the system generalized method of moments (SYS-GMM) and intermediary effect model to introduce four variables, such as: energy efficiency, human capital, industrial structure and energy structure, which were for empirical analysis. From the results, it was shown that: (1) NOx emissions in China have an accumulated effect; (2) new urbanization inhibits NOx emissions, whilst the agglomeration of energy-intensive industries intensifies NOx emissions. New urbanization weakens the negative impact of the agglomeration of energy-intensive industries on NOx emissions reduction and, (3) among the impacts of new urbanization on NOx emissions, the energy efficiency and human capital reflect the intermediary effect mechanism. At the same time, in the impact of the agglomeration of energy-intensive industries on NOx emissions, the industrial structure and energy structure show the mechanisms of the intermediary effect and masking effect, respectively.