Seagrass beds and coral reefs are both considered critical habitats for reef fishes, and in tropical coastal regions, they often grow together to form “mosaic” habitats. Although reef fishes clearly inhabit such structurally complex environments, there is little known about their habitat usage in seagrass-coral mosaic habitats. The goal of this study was to examine potential factors that drive habitat usage pattern by juvenile reef fishes. We quantified (1) prey availability, (2) potential competitors, and 3) predators across a gradient of mosaic habitats (n = 4 habitat types) for four dominant carnivorous fishes (lethrinids and lutjanids) in the main recruitment season at Dongsha Island, South China Sea. We found that the coral-dominated habitats had not only a higher availability of large crustacean prey but also a higher abundance of competitors and predators of juvenile fishes. Food availability was the most important factor underlying the habitat usage pattern by lethrinids and lutjanids through ontogeny. The predation pressure exhibited a strong impact on small juvenile lethrinids but not on larger juveniles and lutjanids. The four juvenile fishes showed distinct habitat usage patterns through ontogeny. Collectively, mosaic habitats in the back reef system may be linked to key ontogenetic shifts in the early life histories of reef fishes between seagrass beds and coral reefs.