Abstract: To improve the understanding of extreme precipitation development at smaller time scales in the South China monsoon region, the spatial and temporal distributions of 5-minute extreme heavy rain and the persistent characteristics of extreme rainfall events in flood seasons were analyzed. The 5-minute precipitation observation data were obtained from automatic weather stations from 2013–2021 and compared with the characteristics of hourly extreme precipitation. The results show that the 5-minute extreme precipitation threshold (E_5min) has a significant meridional difference, forming a high-value center in the Pearl River Delta region, with overall little inherent influence from mountainous terrain. However, the 1-hour extreme precipitation threshold (E_1h) decreases from coast to inland areas. The high-value area is located on the windward slope of the southerly wind terrain. In the pre-flood season, E_5min decreases from southwest to northeast and is distributed evenly in the post-flood season. In contrast to the diurnal variation characteristics of E_1h, E_5min values in the pre-flood season all have double peaks (the main peak in the afternoon, with the secondary peak in the morning). Only the three regions adjacent to the Pearl River estuary have double peaks in post-flood season; the rest are unimodal. The longer the average duration of extreme precipitation at each station, the more obvious the spatial differences. The longest durations are on the southern coast east of Yangjiang and the adjacent area of Longmen, followed by the coastal areas west of Yangjiang and the core agglomeration of the Pearl River Delta. The shortest durations are in the north. Further correlating extreme events with spatial and temporal data, it is found that daytime extreme events are more frequent, move faster, and have a wider range than nighttime events, while nighttime events last longer. The speed of inland precipitation systems is higher than that of coastal systems, especially in northwestern Guangdong, resulting in a high 5-minute precipitation efficiency but a low hourly threshold. The durations of extreme precipitation events in the central and southern coastal areas of the Pearl River Delta are the longest (up to 2.30–3.77 hours at night), which may be related to the comprehensive effects of urban agglomeration and sea–land interactions in this region.