Climate change and crop management measures affect crop growth. But their combined and relative impacts on soybean phenology are still not clear. Based on the first-difference method, we discriminated and quantified the impacts of climate change and crop management measures on soybean phenology using observational data from 51 agro-meteorological stations in China's major soybean planting areas from 1992 to 2011. Results showed that (1) vegetative, reproductive and whole growth period of northern spring soybean were shortened whereas those of summer soybean were prolonged. Reproductive and whole growth period of southern spring soybean were also prolonged. (2) Climate change independently prolonged the vegetative growth periods of northern spring soybean, summer soybean, and southern spring soybean by 0.3, 0.52, and 0.3 days/decade, respectively, and shortened the whole growth periods by 1.43, 0.74, and 6.3 days/decade, respectively. Increasing temperature advanced the soybean phenology and shortened key growth stages. (3) Crop management measures contributed more to the observed trends of phenology and growth stages than climate change. Temperature and sunshine duration dominated the impact of climate change on soybean phenology and growth stages. (4) Shifting sowing date and selecting soybean cultivars with high temperature resistance, high thermal requirements and long growth periods are effective strategies to adapt to climate change. The findings could contribute to providing appropriate adaptation and mitigation strategies to facilitate sustainable soybean production.