While new infrastructure, as a technological extension of traditional infrastructure, has important digital economy attributes, mismatched investment in new infrastructure can still be environmentally damaging. To this end, this paper explores the potential impact of the matching relationship between the new infrastructure investment (NII) and the upgrading of industrial structure (UIS) on environmental pollution from the perspective of coupling and coordination between the two. Through a series of quantitative empirical and robustness tests on China’s relevant data from 2011 to 2019, this paper concludes that the coupling coordination level (NUC) of NII and UIS has an inhibitory effect on major environmental pollutants; in terms of mediating effect, NUC can reduce the emission of major environmental pollutants by improving energy consumption structure (ECS) and green innovation level (GII); in terms of nonlinear change characteristics, there is a threshold effect of NUC on the emission of industrial sewage and industrial dust; in terms of spatial properties, NII, NUC, PM2.5 and industrial sewage have positive spatial spillover effects. This study provides theoretical and empirical evidence that can support the government’s decision to implement differentiated new infrastructure investment decisions based on environmental protection, and it also provides a certain level of reference for developing countries to make more environmentally friendly new infrastructure investment decisions.