Taking into account the impact of the three subsystems of flood and sediment transport, social economy, and ecological environment on the development of the lower Yellow River Basin, the combination weight method was used to determine the indicator weights, and a coupling coordination degree model of flood and sediment transport-social economy-ecological environment system was constructed to analyze the trend of coupling coordination changes in the lower Yellow River Basin. The results showed that there were significant differences in the comprehensive development index of the three subsystems in the lower Yellow River Basin from 2000 to 2020. The comprehensive development index of the social economy subsystem increased steadily from 0.079 to 0.239, showing an exponential increase. The development of the ecological environment and the flood and sediment transport system was relatively uneven. The interaction between subsystems is obvious, but the development level of coupling coordination is relatively low, experiencing a transition from moderate imbalance to near imbalance, and there is great room for improvement in the future. Under the high-level coupling relationship, the uneven development of the flood and sediment transportation and ecological environment subsystems is the main reason restricting the improvement of coupling coordination. Among them, the river stability index and flat beach flow in the flood and sediment transportation system are the main factors, followed by the habitat quality index and domestic sewage discharge in the ecological environment subsystem.