The Pearl River Delta (PRD) region is located on the southeast coast of mainland China and it is an important economic hub. The high levels of particulate matter (PM) in the atmosphere, however, and poor visibility have become a complex environmental problem for the region. Air quality modeling systems are useful to understand the temporal and spatial distribution of air pollution, making use of atmospheric emission data as inputs. Over the years, several atmospheric emission inventories have been developed for the Asia region. The main purpose of this work is to evaluate the performance of the air quality modeling system for simulating PM concentrations over the PRD using three atmospheric emission inventories (i.e., EDGAR, REAS and MIX) during a winter and a summer period. In general, there is a tendency to underestimate PM levels, but results based on the EDGAR emission inventory show slightly better accuracy. However, improvements in the spatial and temporal disaggregation of emissions are still needed to properly represent PRD air quality. This study’s comparison of the three emission inventories’ data, as well as their PM simulating outcomes, generates recommendations for future improvements to atmospheric emission inventories and our understanding of air pollution problems in the PRD region.