The Community Multiscale Air Quality (CMAQ) model version 5.3 (CMAQ53), released to the public in August 2019 and followed by version 5.3.1 (CMAQ531) in December 2019, contains numerous science updates, enhanced functionality, and improved computation efficiency relative to the previous version of the model, 5.2.1 (CMAQ521). Major science advances in the new model include a new aerosol module (AERO7) with significant updates to secondary organic aerosol (SOA) chemistry, updated chlorine chemistry, updated detailed bromine and iodine chemistry, updated simple halogen chemistry, the addition of dimethyl sulfide (DMS) chemistry in the CB6r3 chemical mechanism, updated M3Dry bidirectional deposition model, and the new Surface Tiled Aerosol and Gaseous Exchange (STAGE) bidirectional deposition model. In addition, support for the Weather Research and Forecasting (WRF) model's hybrid vertical coordinate (HVC) was added to CMAQ53 and the Meteorology-Chemistry Interface Processor (MCIP) version 5.0 (MCIP50). Enhanced functionality in CMAQ53 includes the new Detailed Emissions Scaling, Isolation and Diagnostic (DESID) system for scaling incoming emissions to CMAQ and reading multiple gridded input emission files. Evaluation of CMAQ531 was performed by comparing monthly and seasonal mean daily 8 h average (MDA8) O3 and daily PM2.5 values from several CMAQ531 simulations to a similarly configured CMAQ521 simulation encompassing 2016. For MDA8 O3, CMAQ531 has higher O3 in the winter versus CMAQ521, due primarily to reduced dry deposition to snow, which strongly reduces wintertime O3 bias (2-4 ppbv monthly average). MDA8 O3 is lower with CMAQ531 throughout the rest of the year, particularly in spring, due in part to reduced O3 from the lateral boundary conditions (BCs), which generally increases MDA8 O3 bias in spring and fall ( 0.5 μg m-3). For daily 24 h average PM2.5, CMAQ531 has lower concentrations on average in spring and fall, higher concentrations in summer, and similar concentrations in winter to CMAQ521, which slightly increases bias in spring and fall and reduces bias in summer. Comparisons were also performed to isolate updates to several specific aspects of the modeling system, namely the lateral BCs, meteorology model version, and the deposition model used. Transitioning from a hemispheric CMAQ (HCMAQ) version 5.2.1 simulation to a HCMAQ version 5.3 simulation to provide lateral BCs contributes to higher O3 mixing ratios in the regional CMAQ simulation in higher latitudes during winter (due to the decreased O3 dry deposition to snow in CMAQ53) and lower O3 mixing ratios in middle and lower latitudes year-round (due to reduced O3 over the ocean with CMAQ53). Transitioning from WRF version 3.8 to WRF version 4.1.1 with the HVC resulted in consistently higher (1.0-1.5 ppbv) MDA8 O3 mixing ratios and higher PM2.5 concentrations (0.1-0.25 μg m-3) throughout the year. Finally, comparisons of the M3Dry and STAGE deposition models showed that MDA8 O3 is generally higher with M3Dry outside of summer, while PM2.5 is consistently higher with STAGE due to differences in the assumptions of particle deposition velocities to non-vegetated surfaces and land use with short vegetation (e.g., grasslands) between the two models. For ambient NH3, STAGE has slightly higher concentrations and smaller bias in the winter, spring, and fall, while M3Dry has higher concentrations and smaller bias but larger error and lower correlation in the summer.