To understand the impact of the impoundments of the Three Gorges Reservoir on the fish community structure in the Jiangjin section, the commercial catch surveys were conducted from 2006 to 2012. In total 3 orders, 10 families, 45 genera and 67 species were identified. Cluster analysis (CA) separated the different annual species composition into two groups. One group was comprised of the data from the year 2006/2007/2008/2010, and the other group contained the data from 2011/2012. The number of species declined after the operation of the 175 m sluice of the Three Gorges Reservoir in 2010. No significant difference between the two groups was observed by the method of oneway ANOSIM (R=0.96, P=0.07). The fish community structure data for the six years were divided into two groups by using CA and non-metric multidimensional scaling (NMDS) methods. No obvious difference between these two groups (R=1.00, P=0.07) was found by the oneway ANOSIM analysis. The similarity percentage (SIMPER) analysis showed that abundances of the Cobitidae and Homalopteridae decreased, while the abundances of fish adapting to the static or slow flow increased. In brief, the 175 m sluice of the Three Gorges Reservoir brought the greater impact on the fish community structure in the Jiangjin section than the other previous sluices.