The Healthy China Initiative is a major health strategy being pursued by the country. To prevent and control different types of diseases as well as their complex variants, research on the spatio-temporal differentiation among and mechanisms of influence of epidemic diseases is growing worldwide. This study analyzed monthly data on the incidence of influenza by using different methods, including Moran’s
I
, the hotspot analysis model, concentration analysis, and correlation analysis, to determine the characteristics of spatio-temporal differentiation in the incidence of influenza across prefecture-level cities in China from 2004 to 2017, and to examine its relationship with air pollution. According to the results, the overall incidence of influenza in China exhibited a trend of increase from 2004 to 2017, with small peaks in 2009 and 2014. More cases of influenza were recorded in the first and fourth quarters of each year. Regions with higher incidences of influenza were concentrated in northwestern and northern China, and in the coastal areas of southeastern China. Over time, the distribution of regions with a higher incidence of influenza has shifted from the west to the east of the country. A significant relationship was observed between the incidence of influenza and factors related to air pollution. The contents of five air pollutants (PM
2.5
, PM
10
, SO
2
, NO
2
, and CO) were significantly positively correlated with the incidence of influenza, with a decreasing order of contribution to it of SO
2
> CO > NO
2
> PM
2.5
> PM
10
. The content of O
3
in the air was negatively correlated with the incidence of influenza. The influence of air pollution-related factors on the incidence of influenza in different regions and seasons showed minor differences. The large-scale empirical results provided here can supply a scientific basis for governmental disease control authorities to formulate strategies for regional prevention and control.