In reservoir ecosystems, both macroinvertebrates and plankton play an important role in the matter cycling by interactions in food webs. Nanwan Reservoir and Tangpu Reservoir are deep reservoirs with eutrophication and long-term thermal stratification. In this study, these two reservoirs for drinking water supply were investigated to compare their trophic status, macroinvertebrate community structure, stranding crops and biodiversity. The macroinvertebrate communities were quantitatively assessed by Integral index of communities state (IICS) index, and the relationship between the density of plankton and IICS was explored by a PLS model, Spearman rank correlation and regression charts. The results showed that the trophic state index of Nanwan Reservoir was higher than that of Tangpu Reservoir, oligochaetes dominated in Nanwan Reservoir while chironomids did in Tangpu Reservoir. The collectors dominated in Nanwan Reservoir, where their proportion was much higher than Tangpu Reservoir. In deep reservoirs with thermal stratification, eutrophication aggravated the anoxic or anaerobic status at the reservoir bottom, resulting in the periodic anoxic disturbance to macroinvertebrates and reduced standing crops and biodiversity. The relationship between plankton and macroinvertebrate community shifting from positive correlation to negative one was related to the aggravation of reservoir eutrophication. The deterioration of the benthic habitat environment caused by the intensification of eutrophication and the food shortage caused by plankton's avoidance of unfavorable environment were the fundamental reasons for the sustained decline of macroinvertebrate population. Therefore, the reservoir eutrophication can be detected by exploring the relationship between macroinvertebrate and plankton community, for the aim of providing more valuable reference information to reservoir management.