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Abstract This paper describes the atmospheric component of the US Department of Energy's Energy Exascale Earth System Model (E3SM) version 3. Significant updates have been made to the atmospheric physics compared to earlier versions. Specifically, interactive gas chemistry has been implemented, along with improved representations of aerosols and dust emissions. A new stratiform cloud microphysics scheme more physically treats ice processes and aerosol‐cloud interactions. The deep convection parameterization has been largely improved with sophisticated microphysics for convective clouds, making model convection sensitive to large‐scale dynamics, and incorporating the dynamical and physical effects of organized mesoscale convection. Improvements in aerosol wet removal processes and parameter re‐tuning of key aerosol and cloud processes have improved model aerosol radiative forcing. The model's vertical resolution has increased from 72 to 80 layers with the extra eight layers added in the lower stratosphere to better simulate the Quasi‐Biennial Oscillation. These improvements have enhanced E3SM's capability to couple aerosol, chemistry, and biogeochemistry and reduced some long‐standing biases in simulating tropical variability. Compared to its predecessors, the model shows a much stronger signal for the Madden‐Julian Oscillation, Kelvin waves, mixed Rossby‐gravity waves, and eastward inertia‐gravity waves. Aerosol radiative forcing has been considerably reduced and is now better aligned with community best estimates, leading to significantly improved skill in simulating historical temperature records. Its simulated mean‐state climate is largely comparable to E3SMv2, but with some notable degradation in shortwave cloud radiative effect, precipitable water, and surface wind stress, which will be addressed in future updates.