As one of the most productive areas in the Southern Ocean, the Ross Sea is an ideal region for studying of Antarctic marine biological resources and the controlling mechanisms for their distributions. In this study, we focused on the physical and biological control of aggregations and transports of three species (Antarctic krill, crystal krill and Antarctic silverfish) in the Ross Sea in summer. We analyzed the role of chlorophyll and sea ice distributions on the aggregation of these species. Lagrangian Coherent Structures (LCS) analysis was performed on the simulated flow fields from a coupled ocean-sea ice-ice shelf model in the Ross Sea, to investigate the effects of surface flows on mass transport which explains the mechanisms influencing the bio-aggregation. The results show that the aggregations of the three species are generally located in the area with low sea ice concentration as the open water can enhance the irradiance available to primary production. The aggregations are also affected by physical processes. Convergent flow structures in the northwestern Ross Sea and the coastal area off the Victoria Land allow the aggregation of Antarctic krill larvae, and the circular transport barrier near the Terra Nova Bay confines the larval movements of crystal krill and Antarctic silverfish within the Bay. As the convergent structure evolves into two small circular transport barriers, the biomass of Antarctic krill are split into two groups, forming two biological hotspots respectively in the northern and southern sections of the northwest shelf.