In order to promote the precise governance of air pollution in the Yellow River Basin(YRB), it is of great significance to reveal the spatio-temporal patterns of urban air pollution in the basin and its spatial mismatch characteristics with air pollutant emissions. Based on spatial autocorrelation model and spatial mismatch model, this paper selected air pollution-related monitoring data from 69 cities in YRB from 2015 to 2020 as samples, and used ArcGIS, Stata, GeoDa and other softwares to analyze the spatio-temporal patterns of urban air pollution and its spatial mismatch characteristics with air pollutant emissions in YRB. The results showed that: (1) Temporally, the average annual Air Quality Index (AQI) values of cities in YRB ranged from 78.22 to 97.08 in 2015–2020, among which, the average annual AQI values of cities in the upper, middle and lower reaches of the basin decreased from 79.86, 89.23 and 122.14 in 2015 to 66.87,82.98 and 98.43 in 2020. (2) Spatially, there were obvious spatial differences in urban air pollution in YRB, and the AQI was roughly distributed in a geographical gradient of upper reaches < middle reaches < lower reaches, and there were significant spatial correlations in urban air pollution, mainly showing ‘high-high’ and ‘low-low’ aggregating characteristics. Among them, the lower reaches of YRB had formed a concentrated ‘high pollution zone’. (3) There was an obvious spatial mismatch between urban air pollution and air pollutant emissions in YRB, among which the spatial mismatch was obvious in cities such as Wuhai, Zibo, Shizuishan, Yangquan, Taiyuan, Datong, Jiyuan, Kaifeng, Puyang and Xi’an. (4) To improve the overall situation of air pollution in the cities of YRB, this paper proposed that the geographical gradient difference of air pollution in the upper, middle and lower reaches of YRB needs to be fully considered, following the principle of ‘focused treatment, gradual progress, enhanced prevention’, and according to the spatial mismatch characteristics of urban air pollution and air pollutant emissions, it is necessary to build a ‘differentiated’ governance strategy system for urban air pollution in the basin, which is ‘tailored to local conditions and categorized measures’.