The relationship between day-to-day variability of equatorial plasma bubbles (EPBs) and the neutral atmosphere is studied. This study is based on the previous study in which the GPS scintillation index and the tropospheric cloud-top temperature are used as proxies for EPB activity and atmospheric perturbations, respectively, and a correlation was found between their day-to-day variations. In this paper, we maintained the same GPS scintillation data but substituted the atmospheric data via an assimilation run of the Ground-to-topside model of Atmosphere and Ionosphere for Aeronomy (GAIA). Cross-correlation between the EPB activity and the atmospheric temperature is similar to the results in Ogawa et al. (Earth Planets Space 61:397–410, 2009). The new findings from our study include (1) an enhanced correlation between the EPB activity and the neutral atmosphere is found in horizontally and vertically large areas, (2) the longitudinal disturbance of atmospheric temperature and wind velocity during the EPB-active days is enhanced, and (3) the enhancement of atmospheric disturbance during the EPB-active days shows a similarity to the characteristics of large-scale wave structures in the ionosphere. These results more clearly support couplings between EPBs and the neutral atmosphere.