The Songhua River, the largest tributary of the Heilongjiang River, flows through Jilin and Heilongjiang province. The Harbin section of the Songhua River starts from the upstream of Zhu Shuntun and ends at the Dadingzi Mountain in the lower reaches. It is an important water resource for industrial, agricultural and domestic use in Harbin city. Recent years, the intensively anthropogenic activities have resulted in water pollution. The water quality and biodiversity of Harbin section of the Songhua river has been attracted wide attention. At present, more and more studies focused on phytoplankton diversity and community structure. However, the study on phytoplankton in Harbin section of the Songhua River is still in its infancy. To explore the phytoplankton community structure and its relationship with environmental factors in Harbin section of the Songhua River, multivariate statistical analysis was conducted in this study. All sampling sites of Harbin section of the Songhua River were divided into two parts, sampling sites under intense human disturbance and other less polluted sites. A total of 14 sampling sites, the phytoplankton community and 10 environmental parameters were investigated in the spring (April), summer (July), and autumn (October) of 2018. The spatial and temporal distribution differences of phytoplankton community were analyzed by analysis of similarity (ANOSIM). The key species with contribution to the spatio-temporal patterns were identified by similarity percentage (SIMPER) analysis. Additionally, the redundancy analysis (RDA) based on dominant species and 10 environmental variables revealed the ecological distribution of phytoplankton community and identified main factors. The results showed that a total of 136 species of phytoplankton were detected, including 15 dominant species. The species composition was dominated by Bacillariophyta and Chlorophyta (76%), followed by Cyanobacteria (12%), Cryptophyta (7%) and others. Compared with the past 10 years, the community structure belonging to Bacillariophyta-Chlorophyta was relatively stable. Among the three seasons, except for the physical and chemical indicators of specific conductivity (SpCond.), oxidation-reduction potential (ORP) and total phosphate (TP), others were significant differences (P<0.05). During the study, the abundance of phytoplankton in Harbin section of the Songhua River was 7.92×10⁶-21.76×10⁶ ind./L, and the average was 15.27×10⁶ ind./L. The independent sample t-test showed that there were significant differences in total nitrogen (TN), chemical oxygen demand (COD_Mn) and chemical oxygen demand (BOD₅) among the sampling sites affected by human disturbance and other sites (P<0.01). Additionally, there was significant difference of SpCond. at the 0.01 level in different sites, while other physical indicators such as pH did not change greatly (P>0.05). ANOSIM and SIMPER analysis showed that seasonal changes and human-induced disturbances in Site 4 to Site 7 had effects on the spatial and temporal patterns of phytoplankton community. The spatial distribution of Cyanobacteria species was significantly affected by human activity. The results of RDA analysis found that the distribution characteristics of phytoplankton were closely related to the spatio-temporal heterogeneity of water environment. SpCond., TP, turbidity (Tur.) and pH were the key driving factors of phytoplankton community in Harbin section of the Songhua River.