Two sampling zones and six sampling points were set up in the Macao Cotai Ecological Reserve in January, April, July and October 2013-2021 to investigate and analyze the spatial and temporal changes in the zooplankton community structure, and to make a preliminary assessment of the disturbed status of the water body. The results showed that 171 species of zooplankton(including 9 types of zooplankton larvae) were identified in the Cotai Ecological Reserve, of which 156 species were identified in Zone I and 116 species were identified in Zone II. The zooplankton belonged to 8 taxa, and the main dominant taxa were rotifers(57 species), copepods(48 species), and ciliates(33 species); the abundances of the zooplankton in Zone I ranged from 6.00-240.33 ind/L with an average of (59.27±58.39) ind/L, and zooplankton abundance in Zone II ranged from 3.00 to 62.58 ind/L, with an average of (19.20±16.82) ind/L. Regional differences in the structure of zooplankton communities in Zones I and II were significant, with the number of species and abundance in Zone I significantly greater than those in Zone II. The Shannon-Winner diversity index, the Margalef richness index, and Pielou evenness index in Zone I were significantly smaller than those in Zone II, and the interannual variation of zooplankton abundance in Zone I is larger than that in Zone II, which shows that the environment of Zone I is more sensitive than that of Zone II, and that Zone I is more affected by human activities. The dominant zooplankton species was mainly rotifers(pollution indicator species) in 2013-2016, and the dominant zooplankton species was mainly copepods(non-pollution indicator species) in 2017-2021, with a turnover rate of 100%. Except for Shannon-Winner diversity index of Zone I in 2017-2021, which was less than that in 2013-2016, the biodiversity indices of the two zones were greater than those of 2013-2016, which suggests that there has been an improvement in water quality of the reserve.