Diel vertical migration (DVM) of zooplankton plays a large role in the active transport of organic matter to the deep ocean. To unveil the active migration population and their potential roles in biological pump, we studied the diel vertical distribution and metabolic activity of the mesozooplankton at the continental shelf (station C6) and slope (station C9) of the Northern South China Sea. At each studied site, mesozooplankton were collected every 6 hrs over 24 hrs by vertical hauls of 2 or 3 depth strata with 200μm-mesh plankton nets. The triplicate net tows were used for microscopic, rDNA and rRNA analysis, respectively. rRNA and rDNA were used to characterize the metabolic activity and relative abundance of each group. Eukaryotes-universal primers embracing V4 region of 18s rDNA were applied to generate more than 100K metabarcodes per rDNA or rRNA sample. Clustering at 97% identity yielded 10,110 OTUs, of which 6,573 were represented by more than two reads and 620±132 OTUs were identified for each sample. Metabarcodes were mainly represented by 11 groups of metazoan and protist, with Copepoda as the most abundant (65.1-96.3%) in most of the samples, followed with Tunicate at C6 (0.6-19.5%) and Hydrozoa at C9 (0.1-28%) , respectively. The community structure of mesozooplankton at C6 and C9 was significantly different with <40% similarity. Vertical community structure of different depth strata was similar at noon and midnight, while differed significantly at dawn and dusk, indicating that DVM is regulated by diel variations in solar illumination. Diel vertical distribution suggested that DVM occurred mainly at <200m strata at night with Copepoda migrated upward while Hydrozoa migrated downward suggesting different strategies in utilizing food sources. Analyses of rRNA: rDNA ratio showed that the metabolic activity of rare group (rDNA relative abundance <0.01%) was generally higher than that of the abundant group (>1%), among which Acantharia, Ciliaphora and Annelida showed the highest rRNA: rDNA ratio.