The mainstem of Weihe River and its tributaries in the northern foot of Qinling Mountains are located in the ecologically fragile area at the junction of the Loess Plateau and the foothills of Qinling Mountains which are vital for maintaining ecosystem stability. As the primary producer in aquatic ecosystem, phytoplankton plays an important role in maintaining ecosystem stability. In this paper, systematic surveys on water environment and phytoplankton were carried out in the Weihe River mainstem and its five tributaries from the northern foot of the Qinling Mountains in autumn 2017 and spring 2018. First of all, the collected samples were identified, and the concept of functional group was used to divide the phytoplankton in Weihe River Basin. Referring to the 40 groups of functional group division method perfected by Padisák, a total of 25 groups of functional groups were divided into functional groups. The species with relative biomass of more than 5% in each sample were specified as representative functional groups, and the main representative functional groups were 15 groups, namely, A, C, D, N, N_A, MP, T_C, T_B, X3, X1, Y, F, J, L_O, and W1. Then, the water quality of the research area was evaluated by Qr index and Shannon-Wiener index, and it was found that the changes of water quality reflected by the two indexes were not consistent. By comparison and analysis of the two methods, the Qr index is more suitable for evaluating the water quality of the typical tributaries in the northern foot of the Qinling Mountains. The Shannon-Wiener index is more suitable for evaluating the water quality of the Weihe River. The water quality of the typical tributaries in the northern foot of the Weihe River did not obviously change from autumn 2017 to spring 2018, and the water quality of the mainstem of the Weihe River was gradually improved. According to the results of Redundancy analysis (RDA), the main environmental factors affecting the characteristics of phytoplankton functional groups in autumn 2017 and spring 2018 were water temperature, pH, nitrite nitrogen and turbidity, electrical conductivity, and nitrate nitrogen. In this study, the main tributaries with different habitats in the Weihe River Basin were selected as the object, the application of different water quality evaluation methods was deeply explored, and the evaluation system linking biology and water quality was improved. Finally, the results of this study are useful for the ecological management and conservation of the mainstem and tributaries of the Weihe River Basin.