Abstract Sporadic E (Es) layer plays essential role in ionosphere‐atmosphere coupling. Theoretical simulations show that the atmospheric gravity waves (GWs) in the lower thermosphere are the main modulatory source on Es dynamics at small spatial scales and short periods. Based on Sanya Incoherent Scatter Radar, direct observational evidence for the mesoscale GW modulations on low‐latitude Es layer is firstly obtained by four‐dimensional electron density with extreme fine resolutions of 37.5 m in range and 50 s in time. The wave‐like horizontal structures, with ∼10 min period and ∼55 km wavelength, indicate the typical features of mesoscale GWs. Our results confirm that, interacting with the background tidal winds, the upward propagating GWs modulate the horizontal structures and drift velocity of Es layers at different altitudes with increasing amplitude to cause the rapid oscillations in range.