Recent evidence suggests that climate change affects the biodiversity, structure, and function of marine ecosystems, a phenomenon known as marine ecosystem transition. Climate change is expected to increase the frequency of regime shift phenomena, and it often interacts with fishing, contributing to these shifts in marine ecosystems. The ecosystem of the South China Sea lies at the intersection of the north-south air flow, with the Pacific Ocean to the east and the Indian Ocean to the west. It is located at the confluence of Walker Circulation patterns influenced by the Indian and Pacific oceans and is the most complex region in the global climate system and the most sensitive region for large-scale air-sea interaction. Currently, most studies on the response of the fishery ecosystem to climate change in the South China Sea focus on the species level, with a few studies on the fishery ecosystem. Therefore, this study examined the long-term changes in the fishery ecosystem structure in the South China Sea. The study aimed to explore the dominant and main driving factors that promote these long-term changes and support the management and sustainable development of fishery resources within this ecosystem. This study obtained catch data of each species in the South China Sea fishery ecosystem from 1950 to 2019 based on Sea Around US and screened and preprocessed the data. The nutrient levels for various species were obtained from the preprocessed biodiversity database in Sea Around US and were categorized into five functional groups: medium pelagics, small pelagics, medium demersals, shrimps, and medium reef assoc. fish based on previous studies. The optimum temperatures for these species were sourced from previous studies, FishBase and SeaLifeBase, and were classified into three thermal groups: warm-, temperate-, and cold-water species. Using the catch data of different functional and thermal groups, the long-term change characteristics of fishery ecosystem structure in the South China Sea from 1950 to 2019 were systematically determined by multivariate statistical analysis (serial T-test, cumulative sum method, principal component analysis, and temporal cluster analysis), to determine the occurrence of regime shifts. The results showed that the catch in the South China Sea gradually increased, with China’s catch accounting for the largest portion. Since 1981, the number and power of motorized fishing vessels in the South China Sea have increased steadily and stabilized after 1990, whereas the number and tonnage of non-motorized fishing vessels have notably decreased. The regime shift of the fishery ecosystem in the South China Sea occurred in the mid-1980s, mid-1990s, and early 2010s, effectively reflecting the fishing conditions of those periods. However, climate change is a notable contributor to regime shifts in fishery ecosystems. In future studies, factors such as climate change and fishing should be considered comprehensively to explore the leading factors affecting changes in the South China Sea fishery ecosystem and provide a basis for formulating fishery management policies.