Abstract Thunderstorms could cause the irregularities of electron density distributions in the ionosphere by exciting gravity waves and modifying ambient electric field (E‐field). By comparing the DPS‐4D ionosonde observation at 5‐min resolution at Fuke Station in Hainan, China with the lightning detection data, we studied the F‐layer responses to a thunderstorm on 16 August 2016. The results show that the variation in the F‐layer electron density corresponded, with ∼5‐min delay, to the time‐resolved lightning occurrence; the observed temporal delay likely reflects the E‐field modifications associated with charge separation within thunderclouds. After the peak lightning activity, a weak spread‐F appeared alongside sudden rises in plasma drift velocities. These features suggest that lightning disruptions affect ionospheric E‐fields, drive E × B drifts, and cause irregularities in F‐layer electron density via Rayleigh‐Taylor and E × B instabilities. It is the first high‐resolution ionosonde observation of thunderstorm‐induced F‐layer disturbances at low latitudes, providing more insights into the troposphere‐ionosphere coupling.