The South China Sea is the deepest and largest continental shelf marginal sea of China, rich in abundant deep-sea fishery resources. Understanding and mastering the characteristics of the deep-sea ecosystem in the South China Sea is the foundation for the exploitation and conservation of its deep-sea fishery resources. Based on survey data of deep-sea fishery resources and environment in the South China Sea from 2019 to 2020, we divided the pelagic ecosystem of the deep South China Sea into 20 functional groups and constructed an Ecopath model with the Ecopath with Ecosim 6 software. We analyzed the food web structure, energy flow and system characteristics of the ecosystem, and evaluated the fishing carrying capacity of major bulk biological resources including large tuna, Auxis spp., bonitos, carangids, Sthenoteuthis oualaniensis and lanternfishes. The results show that the trophic levels of the deep pelagic ecosystem in the South China Sea present a pyramid-like structure, ranging from 1.00 to 3.87. For the system energy transfer efficiency, the detrital source accounted for 9.974%, the primary producer source for 10.300%, and the overall energy transfer efficiency was 10.150%. The ratio of total primary production to total respiration (TPP/TR) was 2.019, the connectance index (CI) was 0.403, and the system omnivory index (SOI) was 0.214. The fishing carrying capacity of large tuna, Auxis spp., bonitos, carangids, S. oualaniensis and lanternfishes was 19 410, 148 500, 172 050, 730 500, 4 147 500 and 20 655 000 t, respectively. S. oualaniensis and lanternfishes have great fishing potential and can serve as important fishing targets for the future exploitation of deep-sea fishery resources in the South China Sea.