Two acoustical surveys were conducted using a Simrad EK60 scientific echosounder (38 kHz split-beam transducer) in the Nansha, Zhongsha, and Xisha areas during spring 2013 and 2014 to explore the abundance and spatiotemporal distribution of mesopelagic fish species in the central-southern part of the South China Sea. The abundance and distribution were estimated using the echo-integration method based on acoustic data and mid-water trawl samples. We identified 79 fish and squid species in 60 genera, 37 families, 16 orders, and 3 classes in the Zhongsha and Xisha areas during spring 2014. Osteichthyes was the most abundant (65 species), followed by Coleoidea (13 species), and Chondrichthyes was only represented by one species. Stomiidae, Myctophidae, and Gonostomidae (Osteichthyes) were the most abundant families and were represented by 20, 13, and 6 species, respectively. The nautical area scattering coefficient (NASC, m²/nmi²) of mesopelagic fish in the Nansha area was much lower than that in the Zhongsha and Xisha areas, and the former presented more obvious ascending intensity at night. The NASC composition of fish living in 10-200 m depth range at night was not different from that of fish living in 200-1000 m during the day in the Nansha area in spring of 2013, but the difference was significant in the Zhongsha and Xisha areas in spring of 2014. The NASC composition values of fish living in 200-1000 m during the day for the different latitude scopes in the Nansha, Zhongsha, and Xisha areas were significantly different. The NASC of mesopelagic fish in the central-southern part of the South China Sea was (2387±601) m²/nmi². We estimated the abundance of mesopelagic fish in the central-southern part of the South China Sea to be (82±21) million tons based on the existing mesopelagic fish target strength parameters and the median value. These results indicate that the NASC of mesopelagic fish in the central-southern part of the South China Sea was 29.2% higher than the global average. Mesopelagic fish are a potential major strategic fishery resource and are very important for China to develop.