Tuna is a high-speed swimming species with migratory behavior. As rapid swimming often involves large amounts of energy consumption, the oxygen absorption efficiency of gills is crucial to tuna mobility. However, our current understanding of the histological characteristics of gills is far from sufficient to understand the cost-efficiency of oxygen uptake in tuna. In this study, the microstructure, surface ultrastructure, and internal ultrastructure of juvenile and adult yellowfin tuna in the northern South China Sea were studied using optical microscopy, scanning electron microscopy and transmission electron microscopy. The results showed that the top of the filaments of yellowfin tuna was bent, with different cell types on the surface of gill arch, filament, and gill rake. Surface ultrastructural studies showed that gills had high lamellar density, unique oblique blood flow patterns and gill fusion characteristics, and significant differences between juvenile and adult gills structures. The pavement cells (PVC) covered the filament epithelium and lamellae of the gills, with microvilli or microridges at the top. The gills of adult fish had higher cytoplasmic density than those of juvenile fish. Ionocytes were mainly distributed in the lamellae and the base of the lamellae. The top part of gills of the ionocytes of juvenile fish was comprised of microvilli, and adult fish were pit-shaped. Based on these results, the gills rake of juvenile and adult fish are likely to act as a selective barrier and play a role in predation. Rectangular gill lamella, an oblique blood flow pattern, and gill fusion all enable a greater supply of oxygen for yellowfin tuna, which promotes a high oxygen absorption efficiency, thereby meeting its energy requirements for high-speed swimming. In addition, the two main cells of gill epithelium, the pavement cells and ionocytes, provide a guarantee for the survival, respiration, and energy supply of yellowfin tuna in the ocean environment. Among them, a large number of micro-ridge structures on the surface of pavement cells increase the respiratory surface area of gill lamella and improve the gas exchange efficiency of the gills. A large number of mitochondria in ionocytes produce ATP for ion regulation and self-energy. In conclusion, this study elucidated the histological structure of the gills of juvenile and adult yellowfin tuna, enriching our access to the apparent and microstructure data of yellowfin tuna, as well as providing relevant information regarding the ultrastructure of pavement cells and ionocytes in gills filaments and lamella. Thus, this work provides a basis for the relationship between the specific morphological characteristics of high-speed swimming fish and their high-speed swimming habits.