Phenology is an important indicator of global climate change. Revealing the spatiotemporal characteristics of crop phenology is vital for ameliorating the adverse effects of climate change and guiding regional agricultural production. This study evaluated the spatiotemporal variability of soybean’s phenological stages and key growth periods, and assessed their sensitivity to key climatic factors, utilizing a long-term dataset (1992–2018) of soybean phenology and associated meteorological data collected at 51 stations across China. The results showed that (1) during the soybean growing seasons from 1992 to 2018, the average temperature (0.34 ± 0.09 ℃ decade−1) and cumulative precipitation (6.66 ± 0.93 mm decade−1) increased, but cumulative sunshine hours (− 33.98 ± 1.05 h decade−1) decreased. (2) On a national scale, dates of sowing, emergence, trifoliate, anthesis, and podding of soybean were delayed, while the maturity date showed an advancing trend. The vegetative growth period (− 0.52 ± 0.24 days decade−1) and whole growth period (− 1.32 ± 0.30 days decade−1) of soybean were shortened, but the reproductive growth period (0.05 ± 0.26 days decade−1) was slightly extended. Trends in soybean phenological stages and key growth periods diverged in regions. Soybean phenological stages were delayed in Huang-Huai-Hai soybean zone, whereas advanced in southern soybean zone. Moreover, the key growth periods were greatly shortened in northern soybean zone. (3) In general, the sensitivity of soybean key growth periods to temperature was negative, whereas those to precipitation and sunshine hours differed among regions. In particular, most phenological stages were negatively sensitive to sunshine hours. Our results will provide scientific support for decision-making in agricultural production practices.