Cobia (Rachycentron canadum) is an increasingly important marine fish with significant potential for aquaculture in China. Several studies have shown that this fish exhibits distinct locomotion patterns, feeding behaviors and nutritional demands during the larvae and juvenile stages. In order to explore the developmental characteristics of the spine and appendage bones in the early stages of cobia, this paper described the morphologic ossification characteristics of the vertebrae and appendages of larval and juvenile cobia [1 to 33 days post hatching (dph)] using a cartilage bone clearing and staining technique to obtain information on the structural development and functional adaptation of larvae and juveniles organs. After cartilage and bone were stained with alcian blue and alizarin red, vertebral columns were observed to develop from haemal arches and neural arches at 7 dph. Then, the centrum, haemal arches, and neural arches began to ossify at 13 dph. The dorsal rib and ventral rib began to ossify at 17 and 20 dph, respectively, and the vertebrae were fully ossified at 29 dph. The appendicular skeleton developed in the following order: the pectoral fin is the first to develop, followed by the caudal, ventral, dorsal, and anal fins. The pectoral fin began to develop from the cleithrum at 4 dph. The supracleithrum of the pectoral fin ossified at 12 dph and at the same time, the scapula foramen appeared, while the coracoid and scapula began to ossify at 20 dph. The hypural 1 of the caudal fin appeared at 15 dph, the urostyle, parhypural, and fin ray began to ossify at 15 dph, whereas the hypural began to ossify at 18 dph. The ventral fin plate extended to the cleithrum at 17 dph and simultaneously, the ventral fin began to ossify. At 17 and 18 dph, the dorsal and anal fins were ossified in the same pattern. The appendicular skeleton, with the exception of the urostyle, cleithrum, and pelvic girdle, underwent cartilaginous ossification. The development of the vertebral column and appendicular skeleton, on the other hand, is accompanied by changes in feeding patterns and locomotion patterns, such as the emergence of pectoral fin primordia that created conditions for the beginning of larval movement, the development of tail fin folds that enhanced its swimming ability, and the development of pectoral and tail fins in furtherance of cobia’s quick swimming. The results of the study show that exercise skeletons were preferentially developed, such as ossification of the vertebral column and the appendicular skeleton, which enhanced cobia’s forced swimming ability. In addition, hypural healing has been found during skeletal development. In accordance with this process, this paper considered that the morphotype transition of the caudal fin is associated with hypural healing. It is suggested that the osteological ontogenesis of larval and juvenile cobia is closely related to changes in their movement patterns. At 22 dph, scale outgrowth could be found on the caudal peduncle, the vertebral column and appendicular skeleton tended to be fully ossified, and the body features of the fish are the same as adult fish except for the shape of the caudal fin. This study proposes the use of the start of vertebrae ossification as a criterion to distinguish between larval and juvenile cobia, which are considered to enter the juvenile stage at 13 dph. The results suggest that the early bone developmental characteristics of cobia larvae and juveniles are closely related to their functional adaptation. Research on the development of the vertebral column and the appendicular skeleton of cobia is important to enhance the understanding of environmental preferences and functional morphology.