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Abstract Previous observational and modeling studies have suggested that moisture plays a dominant role in Madden–Julian oscillation (MJO) evolution. Using a realistic MJO simulation by incorporating the role of mesoscale stratiform heating in the Zhang–McFarlane deep convection scheme in the National Center for Atmospheric Research Community Atmosphere Model, version 5.3 (NCAR CAM5.3), this study investigates the factors responsible for the improved MJO simulation by examining moisture variations during different MJO phases. The results of column moist static energy (MSE) and moisture budgets show that during the suppressed phases of MJO, vertical advection acts to increase MSE anomalies for the development of deep convection while radiative heating and surface heat flux decrease MSE. The opposite holds true at the MJO mature phase. However, their roles largely cancel each other, leaving horizontal advection to play a major role in the low-level MSE increase during the suppressed phase of the MJO and MSE decrease after the MJO mature phase. A further analysis combining moisture and temperature budget equations is performed to demonstrate the effects of vertical advection and cloud processes within the column at each level. The vertical profiles of column-confined moisture tendency show that large-scale vertical advection induced by latent heat release and evaporation within shallow convective clouds is also important to the lower-tropospheric moistening during suppressed phases. This confirms the role of shallow convection in low-level moistening ahead of MJO deep convection. Radiative heating is vital across all MJO phases, and its warming effects keep the column humidity anomaly maintained in mature phases. None of these features are reproduced by the standard CAM5.3.