Using the thermosphere‐ionosphere‐mesosphere electrodynamics general circulation model simulations, we investigate the short‐term ionospheric variability due to the child waves and altered tides produced by the nonlinear interaction between the 6 day wave and migrating tides. Via the Fourier spectral diagnostics and least squares fittings, the [21 h, W2] and [13 h, W1] child waves, generated by the interaction of the 6 day wave with the DW1 and SW2, respectively, are found to play the leading roles on the subdiurnal variability (e.g., ±10 m/s in the ion drift and ~50% in the NmF2) in the F region vertical ion drift changes through the dynamo modulation induced by the low‐latitude zonal wind and the meridional wind at higher latitudes. The relatively minor contribution of the [11 h, W3] child wave is explicit as well. Although the [29 h, W0] child wave has the largest magnitude in the E region, its effect is totally absent in the vertical ion drift due to the zonally uniform structure. But the [29 h, W0] child wave shows up in the NmF2. It is found that the NmF2 short‐term variability is attributed to the wave modulations on both E region dynamo and in situ F region composition. Also, the altered migrating tides due to the interaction will not contribute to the ionospheric changes significantly.