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Secondary air pollution, especially ozone (O3) and secondary aerosols, are emerging air quality challenges confronting China. Nitrous acid (HONO), as the predominant source of hydroxyl radicals (OH), are acknowledged to be essential for secondary pollution. However, HONO concentrations are usually underestimated by current air quality models due to the inadequate representations of its sources. In the present study, we revised the Weather Research and Forecasting & Chemistry (WRF‐Chem) model by incorporating additional HONO sources, including primary emissions, photo‐/dark oxidation of NOx, heterogeneous uptake of NO2 on surfaces, and nitrate photolysis. By combining in‐situ measurements in the Yangtze River Delta (YRD) region, we found the improved model show much better performance on HONO simulation and is capable of reproducing observed high concentrations. The source‐oriented method is employed to quantitatively understand the relative importance of various processes, which showed that heterogeneous NO2 uptake on the ground surface was the major contributor to HONO formation in urban areas. Comparatively, photo‐oxidation of NOx is a main contributor in rural areas. The introduction of multiple sources of HONO led to an apparent increase in OH and hydroperoxyl (HO2) radicals. The promoted HO2 levels further increased diurnal O3 concentration by 4.5–12.9 ppb, while secondary inorganic and organic concentrations were also increased by 14%–32% during a typical secondary pollution event. The improved description of HONO emission and formation in the model substantially narrowed the gaps between simulations and observations, highlighting the great importance in understanding and numerical representations of HONO in secondary pollution study. Plain Language Summary: Nitrous acid (HONO) has a vigorous potential to produce hydroxyl radicals, contributing to tropospheric oxidation reactions. However, current air quality models lack detailed representation of HONO‐related processes. We revised a widely‐used air quality model based on recently reported mechanisms. The improved model can reasonably simulate actual HONO concentrations measured in the Yangtze River Delta region, one of the most urbanized city clusters in China. It is identified that the heterogeneous conversion of nitrogen dioxide on the ground surface and photo‐oxidation of nitrogen oxide may play an important role in HONO formation. The modeling result is indicative of the pronounced enhancement of HONO on secondary air pollutants, including ozone and secondary aerosols. This study highlights the critical impact of HONO on deteriorating secondary air pollution in city clusters. Key Points: Incorporating missing sources of HONO in the air quality model helps to better represent the observed magnitude and temporal variations of HONOHeterogeneous uptake of NO2 on the ground surface and photo‐oxidation of NOx are major contributors to HONO formationHONO can significantly deteriorate ozone and secondary aerosol pollution by enhancing atmospheric oxidizing capacity [ABSTRACT FROM AUTHOR]