In 2012, the zooplankton community structure in Harbin section of Songhua River was surveyed, and chemical index evaluation methods were used to assess the condition of water quality. A total of 40 species of zooplankton were found, including 9 species of protozoa, 27 species of Rotifera, 2 species of Cladocera, and 2 species of Copepoda. There are 34 species which could be treated as polluted indicators, in which 10 species are in light level, 6 species are in o-β in middle level, 9 species are in β middle level, 4 species are in β-α middle level, and 5 species are in α middle level. The annual average richness is 1042.0 ind./L, and the biomass is 0.078 mg/L. The common species are Brachionus quadridentatus, Keratella cochlearis and Polyarthra trigla, which are all mesosaprobity pollution indicators. The pollution degree of all kinds at the sample sites is consistent with the seasonal variation and the annual variation, where the water quality of the upstream is better than that of the downstream. The ordination of seasonal pollution degree from strong to weak levels is summer>autumn>spring. Overall evaluation results showed that, Harbin section of the Songhua River has been polluted in middle eutrophication level and in moderately polluted state. This study reflects that the current status of water quality objectively provides the important scientific basis for the Songhua River water quality and ecological assessment, water environment monitoring and water resources management.