The Earth's thermosphere and ionosphere (TI) are characterized by perpetual variability as integral parts of the atmosphere system, with intermittent disturbances from solar and geomagnetic forcing. This review examines how the TI variability is affected by processes originating from the lower atmosphere and implications for quantifying and forecasting the TI. This aspect of the TI variability has been increasingly appreciated in recent years from both observational and numerical studies, especially during the last extended solar minimum. This review focuses on the role of atmospheric waves, including tides, planetary waves, gravity waves, and acoustic waves, which become increasingly significant as they propagate from their source region to the upper atmosphere. Recent studies have led to better understanding of how these waves directly or indirectly affect TI wind, temperature, and compositional structures; the circulation pattern; neutral and ion species transport; and ionospheric wind dynamo. The variability of these waves on daily to interannual scales has been found to significantly impact the TI variability. Several outstanding questions and challenges have been highlighted: (i) large, seemingly stochastic, day‐to‐day variability of tides in the TI; (ii) control of model error in the TI region by the lower atmosphere; and (iii) the increasing importance of processes with shorter spatial and temporal scales at higher altitudes. Addressing these challenges requires model capabilities to assimilate observations of both lower and upper atmosphere and higher model resolution to capture complex interactions among processes over a broad range of scales and extended altitudes. Key Points Review the role of waves from lower atmosphere in thermosphere/ionosphere (TI) variability Elucidate how predictability of the TI is affected by the lower atmosphere Highlight outstanding questions in studying lower/upper atmosphere coupling