The apparent diurnal vertical migration of zooplankton leads to diurnal vertical migration of certain fishes that feed on zooplankton. In order to investigate the effects of an artificial reef on diurnal vertical migration of micro-and meso-zooplankton, we obtained 14 zooplankton samples from diurnal sampling in and outside an artificial reef area in the coastal Fangchenggang City, Guangxi Autonomous Region in November, 2018. The analysis showed that zooplankton compositions were quite similar between the artificial reef site and the control site, with the low species replacement rate and the same dominant species, indicating that the zooplanktons came from the same faunal assemblage. However, influenced by the flow-field effect of an artificial reef, zooplankton abundance and diversity were higher at the reef site than those at the control site. At the control site, zooplankton abundance showed apparent diurnal changes following a sinusoidal trend, with the highest abundance at 16:00 and the lowest at 08:00. There was apparent vertical migration between 4:00 and 20:00, while zooplankton abundance was quite stable from 20:00 to 4:00. At the reef site, due to the effect of horizontal fast flow field above the reef, zooplankton abundance fluctuated with time and no apparent diurnal vertical rhythm was observed. It is believed that higher zooplankton abundance above an artificial reef would enhance the reef's fish-aggregating effect and promote the conversion of zooplankton productivity to fish. Cluster analysis and ordination of the 14 zooplankton samples identified one sample group for the reef site, but two sample groups for the control site, one being mainly composed of phytoplankton feeders following the upward shifts of phytoplankton during the daytime, the other being mainly composed of carnivorous species during nighttime after the phytoplankton feeders migrating downward.