The Huangfuchuan basin is one of the major sources of coarse sediment in the Yellow River and has long been a focal point and challenge for the conservation of soil and water in the Yellow River Basin. In this study, we analyzed the phase differentiation characteristics of water–sediment variations during the flood season in the Huangfuchuan basin using a long-term dataset. We elucidated the complex response relationship between water–sediment variations and meteorological factors and human activities, which is of great significance for revealing the mechanisms of water–sediment variations in the region and establishing a scientific water–sediment regulation system in the basin. Statistical methods such as the Mann–Kendall trend test, Sen’s slope estimation, Pettitt nonparametric test, and principal component analysis were employed to identify and analyze the trends and dominant driving factors before and after the water–sediment variations and abrupt changes in parameters such as rainfall and temperature in the Huangfuchuan basin. Additionally, multiple regression analysis was used to determine the extent of the contribution of climate and human activities to water–sediment variations in the Huangfuchuan basin. The study revealed that the year 2000 was a turning point for water–sediment variations, with decreases of 11.3%, 76.7%, and 85.1% in flood season rainfall, flood season runoff, and flood season sediment transport, respectively. Despite significant changes in the underlying surface conditions of the Huangfuchuan basin, the relationship between flood season sediment transport and flood season runoff remained a power–law relationship. In the absence of obvious abrupt changes in temperature, rainfall, and other meteorological factors, the changes in the underlying surface caused by human activities are the main cause of the changes in runoff and sediment yield in the Huangfuchuan basin. The current level of vegetation restoration in the Huangfuchuan basin is still relatively low, making it difficult to exert stronger control on sediment yield during the flood season. Meanwhile, human activities, primarily based on engineering measures, play a more significant role in the control of soil and water loss in the basin.