With the rapid growth of global climate change and population urbanization, the contradiction of water resources and water security has become increasingly prominent, which has become a key problem restricting the sustainable development of countries and regions, and the impact of land use and cover change on hydrological processes has become the focus of this field. The Yangtze River Basin (YR), as a major ecological and economic development area in China, plays a strategic role in ecological security protection. Because water yield is an important ecological indicator of regional water environmental function, the exploring the effect of land use change on water yield has great significance on revealing and deepening the effect of land use on water environment function. In this study, we explored the response modes of water yield to land use change in the YR area based on water yield module of InVEST model, and the driving factors affecting regional water production were analyzed by multivariate statistical method. The results are as follows:(1) Between 1990 and 2015, the spatial distribution of average water yield in the YR area exhibited the characteristic of lower in the northwest and higher in the southeast. The average water yield between sub-basins showed obviously spatial differences, and the degrees of differences indicated that midstream > downstream > upstream, water yield among sub-basins showed rising trend in spatial differences. (2) The agricultural land and forest land were the main contribution types, and Dongting Lake, Poyang Lake and Jinsha River were the main contributing basins (50%) of the total water yield. (3) Due to the change of land use structure and allocation, the response of water yield exhibited diversity in land type, among which the agricultural land, grassland and unused land had a positively synergistic effects on water yield, while forest land and water area had negatively synergistic effect, and the construction land to water yield was not obvious. (4) Construction land, water area, population density, Gross Domestic Product, and rainfall were identified as the main driving forces, while the agricultural land, vegetation cover and temperature were identified as the potential driving forces. The regulation of water yield function in the Yangtze River Basin should pay more attention to the spatial difference of water yield among different sub-basins, and coordination between water yield spatial difference and the configuration of land use structure.