AbstractAtmospheric gravity waves (AGWs) and medium‐scale traveling ionospheric disturbances (MSTIDs) in the upper atmosphere affect atmospheric circulation and radio‐wave transmission including satellite positioning and communications, and high‐frequency radio. The 3‐dimensional (3‐D) spectral analysis of airglow images makes it possible to extract wave parameters of AGWs and MSTIDs. Such spectral analysis of long‐term airglow images has not been performed in the southern part of Japan, which is a unique transition latitude from middle to equatorial region. In this study, we calculated the horizontal phase velocity distribution of AGWs in the mesosphere‐lower‐thermosphere (MLT), and MSTIDs in the F‐region ionosphere by applying the 3‐D spectral analysis method to the 557.7 and 630.0‐nm airglow images obtained at Sata (31.0°N, 130.7°E) in Japan over 20 years from 2000 to 2020. The spectra of AGWs in the MLT region in the 557.7‐nm airglow images show that the poleward (northward) power spectral density (PSD) is stronger in summer, suggesting that the tropospheric convection is a possible source of AGWs and the wave ducting propagation occurred. Westward propagation is also observed in winter, suggesting that wind filtering effect by mesospheric jets plays an important role. The PSD of MSTIDs in the 630‐nm airglow images increases during low solar activity periods, suggesting that MSTIDs are produced by ionospheric plasma instability. The westward PSD of MSTIDs is stronger in summer. These results are an important achievement in clarifying the statistical characteristics of AGWs and MSTIDs over Sata, Japan, based on long‐term airglow observations and 3‐D spectral analysis.