In recent years, individual-based model (IBM) has been increasingly used to address issues in marine ecological environment because of its flexibility in incorporating different ecological processes. An IBM regards individual as a simulating unit, considering differences among individuals and influence of variability in spatial and temporal environmental conditions on individual development. This paper provides an overall review of scientific research in ecosystem-based fisheries management and resource recruitment forecasting. We introduced the basic concept, research methods and theory of IBM, and reviewed the status of research with the focus on the applications of larval transport, growth and mortality, prey-predation research using the IBM in fishery. Limitations associated with IBM approach are also discussed. We concluded that it is important for us to conduct interdisciplinary research between scientists in fisheries and other research areas to strengthen and improve our understanding of early life history dynamics for fish species in coastal waters of China, which is essential to develop an ecosystem-based management and assessment of fisheries resources.