Abstract. To evaluate improved emission estimation from online monitoring data, we applied the Models-3/CMAQ (Community Multi-scale Air Quality) system to simulate the air quality of the Yangtze River Delta (YRD) region using two emission inventories without/with incorporated data from continuous emission monitoring systems (CEMS) at coal-fired power plants (Cases 1 and 2), respectively. The normalized mean biases (NMBs) of annual SO2, NO2, O3 and PM2.5 concentrations between observations and simulations in Case 2 were −3.1 %, 56.3 %, −19.5 % and −1.4 %, all smaller in absolute value than those in Case 1, at 8.2 %, 68.9 %, −24.6 % and 7.6 %, respectively. The results indicate that incorporation of CEMS data in the emission inventory helped reduce the biases between simulation and observation and can better reflect the actual sources of regional air pollution. Based on the CEMS data, the air quality changes and corresponding health impacts were quantified for different implementation levels of China's recent ultra-low emission policy. If only the coal-fired power sector met the requirement, the simulated differences in the monthly SO2, NO2, O3 and PM2.5 concentrations compared to those of Case 2, our base case for policy comparisons, were less than 7 % for all pollutants. The result implies only a minor benefit of ultra-low emission control if implemented in the power sector alone, attributed to its limited contribution to total emissions in the YRD after years of pollution control in the sector (11 %, 7 % and 2 % of SO2, NOX and primary particle matter (PM), respectively). If the ultra-low emission policy was enacted at both power plant and industrial boilers, the simulated SO2, NO2 and PM2.5 concentrations compared to the base case were 33 %–64 %, 16 %–23 % and 6 %–22 % lower respectively, depending on the month (January, April, July and October 2015). Combining CMAQ and the Integrated Exposure Response (IER) model, we further estimated that 305 deaths and 874 years of life loss (YLL) attributable to PM2.5 exposure could be avoided with the implementation of the ultra-low emission policy in the power sector in the YRD region. The analogous values would be much higher, at 10,651 deaths and 316,562 YLL avoided, if both power and industrial sectors met the ultra-low emission limits, accounting for 5.5 % and 6.2 % of the totals for the region, respectively. In order to improve regional air quality and to reduce human health risk effectively, coordinated control of various pollution sources should be implemented, and the ultra-low emission control policy should be substantially expanded to industrial boilers and other emission sources in non-power industries.