Abstract This study investigates the roles of neutral winds, composition and atmospheric waves in storm‐time post‐midnight equatorial plasma bubble (EPB) development using the coupled SAMI3‐WACCMX model. Simulations reveal the formation of post‐midnight EPBs extending beyond 1,500 km in altitude and persisting into the post‐sunrise period. The results indicate that disturbance dynamo electric fields (DDEFs) driven by storm time neutral winds dominate the post‐midnight EPB formation. Comparative SAMI3 simulations using NRLMSISE‐2.0 neutral composition under identical neutral wind conditions further demonstrate that thermospheric composition strongly influences EPB distribution, morphology, spacing and occurrence. EPBs also develop in the absence of atmospheric waves, indicating the dominant role of DDEFs in storm‐time EPB initiation. Nevertheless, atmospheric waves regulate EPB morphology and growth through perturbations to vertical E × B drifts, resulting in characteristic EPB spacings comparable to the wavelengths of the underlying atmospheric waves.