Previous studies showed that the density overcooling in the thermosphere during the recovery phases of the October 2003 storms was not reproduced by the National Center for Atmospheric Research Thermosphere‐Ionosphere Electrodynamics General Circulation Model. In this study, a series of controlled numerical experiments were carried out to explore the processes responsible for the neutral density overcooling. It was found that the simulation with the temperature‐dependent reaction rate of N(2D) + O2 from Duff et al. (2003, https://doi.org/10.1029/2002GL016720) can better capture the overcooling during the recovery phases of the October 2003 storms. Our study also demonstrated that the thermosphere recovery strongly depends on the altitudinal distribution of NO emission per mass rather than the NO cooling flux alone. During the storm recovery phases, the temperature starts to show overcooling in 110–180 km where the NO increases primarily, which has great contribution to the density overcooling.