Studying the succession of reservoir ecosystems is of great importance to both freshwater ecosystem research and reservoir management. However, little research has been reported regarding the succession of the Three Gorges Reservoir ecosystem after its impoundment in June 2003. In the present study, we analyzed the macroinvertebrate succession and reservoir zonation of Xiangxi Bay, a tributary of the Three Gorges Reservoir, from August 2003 to July 2010 in different impoundment stages. We found that Chironomidae and Tubificidae were the first to colonize after the first impoundment, with Chironomidae as the main group. Limnodrilus hoffmeisteri dominated the community gradually, and Nais inflata established itself as an additional dominant species from April 2004. The total macroinvertebrate density and richness increased from the first stage, exhibited a spatial pattern of "high in the middle and low in the two edges". The density peaked in April 2006 (24,146 ind./m²), declined remarkably after the second stage of impoundment, and changed slightly after the third stage. Fewer rare species were observed in the third stage than in the other two stages, which indicated that the community became more stable gradually. Two-way indicator species analysis revealed a stable zonation pattern during the first stage; however, the community type changed during the second stage, which implied that the stage was associated with strong disturbance. Afterward, we observed seasonal fluctuations in the community type, which was coupled to seasonal fluctuations of the water level. This indicated that the macroinvertebrate assemblage gradually adapted to the periodic reservoir operation of the Three Gorges Reservoir and that the community structure exhibited stable periodic fluctuations.