AbstractAs a companion study of the Part 1 (J. C. Wang et al., 2022, https://doi.org/10.1029/2022JA030948), the impact of the lower‐thermospheric circulation on atomic oxygen (O) in the mesosphere and lower thermosphere (MLT) region is investigated in this Part 2 using Specified Dynamics Configuration Runs of the Whole Atmosphere Community Climate Model eXtended (SD‐WACCMX) output. The asymmetry of the O profile in the summer and winter MLT region is mainly driven by local vertical advection, which is associated with the lower‐thermospheric winter‐to‐summer circulation and middle‐to‐upper thermospheric summer‐to‐winter circulation. It is found that meridional transport and eddy diffusion only weakly modulate the O budget within this altitude range. The globally and annually averaged transport effect due to the vertical advection is quantitatively estimated. It is shown that the vertical advection is the dominant mechanism in redistributing O at altitudes between 84 and 103 km, suggesting the vertical wind can efficiently transport O between its source and sink region within the vertical column. This study demonstrates that whole atmosphere coupling on seasonal time scales is a complex interaction involving multiple underlying mechanisms within the space‐atmosphere interaction region.