Abstract: The influence of atmospheric waves generated by a tropospheric convective source on the state of the upper atmosphere and ionosphere during the recovery phase of the geomagnetic storm on May 27–28, 2017 is studied. A new approach to accounting for atmospheric waves generated by tropospheric convective sources in large-scale atmospheric models without using wave parameterization is proposed and implemented. The developed approach makes it possible to comprehensively study the effects generated by atmospheric waves against the background of various geophysical events, including geomagnetic storms. The multimodel study shows that the proposed approach allows us to reproduce perturbations of the critical frequency of the ionosphere’s ionospheric F2 layer caused by the propagation of atmospheric waves generated by a tropospheric meteorological source. It is shown that the inclusion of a heat inflow source simulating the propagation of atmospheric waves from the lower atmosphere in the global model enhances the effects of a geomagnetic storm, which manifests itself as an additional decrease in the critical frequency of the F2 layer, which can reach 7% of the absolute values.