The abyssal sea floor of the Clarion-Clipperton Fracture Zone (CCFZ) in the Pacific Ocean is expected to become a commercially important nodule mining area in the near future. Hence, it is crucial to understand the community structure of biological communities there, so that nodule harvesting activities can be designed to minimize deleterious impacts on marine life. Meiofauna is an important component of the abyssal infaunal community but relatively little is known on their biodiversity, abundance, and community structure in the CCFZ. We provide here the first quantitative observations of metazoan benthic animals ≥40 μm in a 30 × 30 km area survey stratum in the Ocean Mineral Singapore contract area at the eastern end of the CCFZ. A total of 88 867 individuals, identified to 23 animal groups, were collected from 12 randomly sampled stations using a multiple corer. Even in our small surveyed area, the meiofaunal community structure appeared different at our stations, confirming that the CCFZ deep sea floor is very diverse. From the top 0–5 cm sediment layer, unsurprisingly, the three most abundant animal groups were the Nematoda (87.9 ± 2.9%), the Nauplii (5.0 ± 1.3%) and the Copepoda (4.3 ± 1.1%). The majority of the meiobenthos (76.6%) were in the top 0–2 cm sediment layer. Our results suggested that substratum shear strength was negatively and significantly correlated to meiofaunal abundances among the 12 stations. Nodule cover and nodule volume did not appear to affect the meiofaunal community structure at the major taxon level. The mean meiofaunal abundance (235.7 ± 26.4 ind./10 cm2) was relatively high at our site in comparison with previous studies elsewhere in the CCFZ, further confirming the westward decrease in meiofaunal abundance across the CCFZ.