Zooplankton is an important primary consumer in the food chain, and its community structure is one of the important indicators for the health evaluation of aquatic ecosystems. A systematic survey of water environment and zooplankton was carried out in the Weihe River mainstem and its five tributaries from the northern Qinling Mountains during autumn 2017 and spring 2018. The nutrient concentrations of the Weihe River mainstem were higher than those of the five tributaries, while turbidity of the mainstem was 10-100 times higher than those of the tributaries. A total of 136 species of zooplankton (65 species of protozoa, 44 species of rotifers, 15 species of cladocerans, and 12 species of copepods) were identified in the two surveys. Among them, the number, density and biomass of zooplankton in the mainstem of the Weihe River mainstem in autumn 2017 were 14 species, 9.02 ind./L and 0.0051 mg/L, while tributaries were 37 species, 42.78 ind./L and 0.0229 mg/L, respectively. The number of species, density and biomass of zooplankton in the Weihe River mainstem in spring 2018 were 52 species, 292.89 ind./L and 0.1734 mg/L, while tributaries were 68 species, 70.15 ind./L and 0.0508 mg/L, respectively. In autumn, the number of zooplankton species, density and biomass in the lower reaches of the Weihe River mainstem were the lowest, while those increasing in the rank from upper, middle, to lower reaches of the Weihe River mainstem in spring. The density and biomass of zooplankton in the Luofu River were the highest in autumn, and those in the Bahe River highest in spring. The difference in dominant species of zooplankton between the trunk and tributaries of spring and autumn is relatively small, but the number of dominant species in autumn is less than that in spring. Canonical correspondence analysis revealed seasonal variance in the dominant factors of the zooplankton community structure in the Weihe River mainstem and the five tributaries. This study not only revealed the correlation between zooplankton community structure and environmental factors in the Weihe River mainstem and its five tributaries, but also provided key data for environmental monitoring and ecological protection in the Weihe River Basin.