Research on the overall social, economic and environmental (SEE) impacts of water resources projects (WRP) has gradually attracted attention. However, the WRP-related indirect impacts as linked through various supply chains from a number of disaggregated sectors and their interactive relationship are rarely studied. Here in this study, under a general disaggregated input-output (IO) framework, a distributive Three Gorges Project input-output (DTGIO) model is developed to investigate the composite effects of Three Gorges Project (TGP) based on a disaggregated TGP-IO table for the Yangtze River economic belt (YREB). DTGIO model could facilitate exploring i) the interactions among key TGP-related effects from production and consumption sides; ii) the impacts of various TGP-induced changes on specific SEE sectors; iii) the detailed TGP water flow paths as induced by the final demand of each province in YREB. It is discovered that the TGP has the greatest impact on agriculture. Although the construction of the TGP submerged a large amount of land and adversely affected agriculture in the reservoir area, its effective flood control function can reduce flooding in the “land of fish and rice” and create favorable conditions for agricultural development. The connection between the TGP and the inner provinces of YREB is mainly realized by the hydropower generation sector. For the economic benefits of the TGP, the economic benefits of the investment of various sectors of the TGP are diversified, which should be adjusted according to the government's objectives. For the ecological effects of the TGP, the interaction of sectors (especially the irrigation service sector and hydropower generation sector on consumption side, and the hydropower generation sector and water supply sector on production side) should be valued and a sense of joint management for the relevant sectors of TGP should be established.