Solar eclipse is a daytime phenomenon that significantly disturbs the ionosphere, but whether the eclipse induces ionospheric irregularities in the nighttime remains unknown. In this study, we analyzed the dense total electron content (TEC) observations from the ground‐based Global Navigation Satellite System receivers over East and South Asia to examine the development of the irregularities in the nighttime on the day of the 21 June 2020 annular solar eclipse. The rate of TEC index (period <5 min) indicates the occurrence of the irregularities that evolve from the large or coarse structures with a period ranging from hours to dozens of minutes in the nighttime due to the eclipse. We take advantage of the data‐adaptive analysis method, Hilbert‐Huang transform, to derive the instantaneous amplitude and frequency of the TEC time series, which exposes the temporal and spatial evolutions of the irregularities from larger structures continuously. Plain Language Summary The moon obscuration of a solar eclipse suddenly reduces solar irradiation in the daytime, which generates large atmospheric and ionospheric perturbations. The massive total electron content observations from the dense ground‐based Global Navigation Satellite System network recorded the occurrence of the large‐scale ionospheric perturbations and plasma irregularities in the nighttime on 21 June 2020. The occurrence of nighttime irregularities due to a solar eclipse was never known. This study further shows that the Hilbert‐Huang transform is an efficient technique to sift out the structures with large, coarse, or fine scales (Figure S1 in Supporting Information S1) from the total electron content time series. This data‐adaptive method benefits capturing the transient evolution of the ionospheric weather. Key Points Development of ionospheric plasma irregularities after the solar eclipse in postsunset hours Evolution of the irregularities from the convergence of large enhancements Hilbert‐Huang transform analysis sifts out the density structures with scales from coarse to fine