The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) is a small-toothed whale endemic to the Yangtze River in China and is the only freshwater population in the genus Neophocaena. To compare and analyze the adaptive changes of YFPs between ex-situ and captive waters, we performed RNA sequencing of YFPs blood tissues for ex-situ and captive population. A total of 1,201 differentially expressed genes (DEGs) were identified, of which 423 were upregulated in ex-situ population and 778 were upregulated in captive population. Gene Enrichment analysis showed that DEGs were generally enriched for visual, digestive and immune system related pathways. Further analysis revealed that several key immune system pathways, such as chemokine signaling pathway and B cell receptor signal pathway, were activated in ex-situ population. In addition, key pathways related to vision, including phototransduction and inflammatory mediator regulation of TRP channels, as well as pathways related to the digestive system, such as protein digestion and absorption and salivary secretion, were activated in captive population. These results suggest that the ex-situ population may have adapted to the complex environmental conditions of semi-natural waters by enhancing their immune function and that the visual function and protein digestion of YFPs have been improved compared to the ex-situ population based on the conditions of artificial feeding, such as higher transparency of the water and regular feeding. This study provides a theoretical basis for evaluating the adaptability of the YFPs to different environment and provide useful reference for the ex-situ and captive protection in the future.