The debates about the extent to which phytoplankton in freshwater ecosystems are regulated by top-down or bottom-up forces have been ongoing for decades. This study examines the effects of bottom-up and top-down factors on the phytoplankton functional groups in a eutrophic lake. Phytoplankton and zooplankton were sampled and physical-chemical variables measured from May 2019 to October 2019 in Lake Hulun, China. Approximately 43 phytoplankton species were observed and grouped into 23 functional groups. For the zooplankton, about 27 species were observed and classified into 8 functional groups. The study revealed that the bottom-up effects of physical-chemical variables on some phytoplankton functional groups was stronger than the top-down effects of zooplankton. Water temperature (WT), total phosphorus (TP), total nitrogen (TN), conductivity (Cond), water transparency (SD), and dissolved oxygen (DO) significant influence the biomass of the phytoplankton functional groups. The biomass of phytoplankton functional groups was influenced positively by nutrient availability likely because nutrients influence the growth and reproduction of phytoplankton in freshwater. WT and DO had a positive influence on biomass of phytoplankton functional groups. Conversely, phytoplankton biomass revealed a decreasing trend when SD and Cond significantly increased. This study showed that zooplankton functional groups were positively correlated with phytoplankton biomass implying that the top-down control of phytoplankton by the zooplankton in the lake is not strong enough to produce a negative effect. It is evident that the zooplankton functional groups in Lake Hulun are controlled more by bottom-up force than top-down.