Based on the use of the coupling coordination model to calculate the coupling coordination degree of carbon emission and pollutant control, the national, regional, and provincial spatiotemporal characteristics of the synergistic effect of pollution control and carbon emissions reduction in China were further analyzed, facilitating the crucial to identification of key areas. The fixed effects regression models and provincial panel data from 2006 to 2020 were used to explore factors contributing to better synergizing the reduction of pollution and carbon emissions in China. On this basis, the adjustment variable of R&D investment intensity was introduced, and the regulation effect model was constructed to further explore the influence mechanism of the synergistic effect of pollution reduction and carbon reduction. The results showed that: synergy exists between carbon emission reduction and the air pollution control system, the evolution of the synergistic effect of pollution reduction and carbon reduction in China presented an inverted "U"-shaped trend from 2006 to 2020, and there was spatial aggregation and a spatial spillover effect in pollution reduction and carbon reduction. The synergistic governance of carbon emission and pollutant control was still at a relatively low level. The carbon emission and air pollutant emission systems were still in an unstable and uncoordinated state. The results showed that: The degree of coordination of eastern China, central China, and western China decreased in turn. At the national level, energy consumption structure, per capita GDP, and the proportion of green investment were the main factors affecting the synergistic effect of pollution reduction and carbon. The heterogeneity of the influencing factors existed in the central, eastern, and western regions on industrial structure, energy consumption structure, energy utilization efficiency, per capita GDP, urbanization rate, the proportion of green investment, and transportation structure. The intensity of R&D played a significant moderating effect in the whole country, eastern, and central regions. However, no significant moderating effect was identified in the western region. In the eastern region, the urbanization rate, the proportion of green investment, and the transportation structure could not have a significant effect on the synergistic effect of pollution reduction and carbon reduction alone, and it must be coordinated with the intensity of R&D.