This modeling study quantifies the daytime low‐latitude vertical E×B drift changes in the longitudinal wave number 1 (wn1) to wn4 during the major extended January 2006 stratospheric sudden warming (SSW) period as simulated by the National Center for Atmospheric Research thermosphere‐ionosphere‐mesosphere electrodynamics general circulation model (TIME‐GCM), and attributes the drift changes to specific tides and planetary waves (PWs). The largest drift amplitude change (approximately 5 m/s) is seen in wn1 with a strong temporal correlation to the SSW. The wn1 drift is primarily caused by the semidiurnal westward propagating tide with zonal wave number 1 (SW1), and secondarily by a stationary planetary wave with zonal wave number 1 (PW1). SW1 is generated by the nonlinear interaction of PW1 and the migrating semidiurnal tide (SW2) at high latitude around 90–100 km. The simulations suggest that the E region PW1 around 100–130 km at the different latitudes has different origins: at high latitudes, the PW1 is related to the original stratospheric PW1; at midlatitudes, the model indicates PW1 is due to the nonlinear interaction of SW1 and SW2 around 95–105 km; and at low latitudes, the PW1 might be caused by the nonlinear interaction between DE2 and DE3. The time evolution of the simulated wn4 in the vertical E×B drift amplitude shows no temporal correlation with the SSW. The wn4 in the low‐latitude vertical drift is attributed to the diurnal eastward propagating tide with zonal wave number 3 (DE3), and the contributions from SE2, TE1, and PW4 are negligible.