It is important to comprehend the evolution of drought characteristics and the relationships between different kinds of droughts for effective drought mitigation and early warnings. The study area was the Pearl River Basin, where spatiotemporal changes in the multiscale water balance and soil moisture at various depths were analyzed. The meteorological data used in this study were derived from the China Meteorological Forcing Dataset, while the soil moisture data were obtained from the ECMWF ERA5-Land reanalysis dataset. The Standardized Precipitation Evapotranspiration Index (SPEI) and Standardized Soil Moisture Index (SSI) were applied to represent meteorological and agricultural droughts, respectively. By using the run theory for drought event identification, the characteristic values of drought events were analyzed. The correlation between the multiscale SPEI and SSI was examined to represent the propagation time from meteorological drought to agricultural drought. This study indicated that while the western part of the Pearl River Basin experienced a worsening atmospheric moisture deficit and the southern part had intensifying dry conditions for soil moisture, the rest of the basin remained relatively moist and stable. Soil conditions were moister in the deeper soil layers. The durations of agricultural droughts have generally been shorter than those of meteorological droughts over the past 40 years. Within the top three soil layers, the severity, duration, and frequency of drought events progressively increased, increased, and decreased, respectively, as soil depth increased. The propagation time scale from a meteorological drought to a four-layer agricultural drought was typically within 1-5 months. This study advanced existing research by systematically analyzing drought propagation times across soil depths and seasons in the Pearl River Basin. The methodology in this study is applicable to other basins to analyze drought complexities under climate change, contributing to global drought resilience strategies. Understanding the spatiotemporal characteristics of meteorological and agricultural droughts and the propagation time between them can help farmers and agricultural departments predict droughts and take appropriate drought-resistant measures to alleviate the damage of droughts on agricultural production.