In order to investigate the various seasonal dynamics of the phytoplankton community and the correlation with environmental factors in the Zhangye section of Heihe River, the samples of the phytoplankton and the aquatic environment from 10 different river segments were assessed in 2017. A total of 316 species belonging to 8 divisions and 91 genera including the variants were identified to be mainly composed of the Chlorophyta, Cyanophyta and Bacillariophyta in the proportions of 10.75%, 15.22% and 68.35%, respectively. The environmental factors such as the temperature, conductivity, salinity, dissolved oxygen and chlorophyll-a displayed significant temporal and spatial changes, while the total nitrogen and total phosphorus showed a significant increase with the decrease in altitude. During the survey period, the density of the phytoplankton in the Zhangye section of Heihe River was 0.92×10⁴-116.67×10⁴ cells/L, with the existence of a significant increasing trend from upstream to downstream. The dominant species mainly belonged to Bacillariophyta and included Meridion sp., Ceratoneis arcus, Achnanthes minutissimum, Diatoma elongatum var. tenuis, Synedra acus, Navicula simplex, Nitzschia palea, Melosira varians, Diatoma vulgaris, Synedra ulna etc. In addition, it was found that Chlorophyta species Microcystis smithii (McNaughton index Y was 0.025), Cyanophyta species Scenedesmus quadricauda (Y value was 0.020) and Cryptophyta species Chroomonas acuta and Cryptomonas ovata (Y values were 0.045 and 0.032, respectively) were prominent in the middle and lower reaches of the river. With reference to the algal diversity in four quarters, the averages of Shannon-Wiener index (H') were 2.65, 2.76, 2.89 and 2.44, while Pielou evenness index (E) were 0.93, 0.90, 0.91 and 0.87 and Margalef diversity index (d) were 1.73, 1.77, 2.00 and 1.31, respectively. With the decrease in altitude, the H' and d were seen to increase significantly while the range of E remained relatively stable. Through the comprehensive evaluations of the water physicochemical index together with the density of algae and their diversity, the water quality in the Zhangye section of Heihe River was found to range from being unpolluted to light or moderately polluted. However, the levels of pollution in the middle reaches appeared to be aggravating. Meanwhile, the results of redundancy analysis and Pearson analysis for the relationship between the phytoplankton and the environmental factors showed that the factors such as total nitrogen, total phosphorus, temperature and elevation played a key role in affecting the structure and dynamics of the phytoplankton community in the Zhangye section of Heihe River. In the downstream regions of the river, factors such as conductivity and salinity were found induce a similar effect on the phytoplankton community structure.