The post-release performance of cultured fish is crucial for understanding the viability of cultured fish and assessing the effects of stock enhancement programs. This study aimed to investigate the initial post-release performance of cultured Cyprinus chilia juveniles by examining their movement, spatial distribution, gut fullness, and gut microbiota in nature. In July 2022, a total of 20,000 C. chilia juveniles, tagged with visible implant fluorescence (VIE), were released into Qilu Lake, a shallow lake in southwestern China. Subsequently, continuous recapture was conducted at fixed recapture sites using trap nets during the first 7 days, one month and three months after release. Out of the released fish, 512 were recaptured, resulting in a recapture rate of 2.56%. The recaptured fish had a 100% tag retention rate. The majority (98.05%) of the recaptured fish were found in the recapture sites located on the eastern or western lakeshore, while only 10 fish were recaptured from the recapture sites in the northern lake area. The water depth range where the recaptured fish were found ranged from 190 to 350 cm, with most fish preferring depths less than 300 cm. The majority of the released fish migrated towards the eastern and western lakeshore, with long-distance movement (greater than 100 m) primarily occurring within the first four days after release. The level of gut fullness in the released fish initially decreased and then increased over time following release. Regarding gut microbiota, the dominant phyla observed in most samples were Firmicutes, Proteobacteria, Cyanobacteria, and Fusobacteria. Furthermore, significant variations in the dominant genera were observed across different samples. Principal coordinates analysis (PCoA) revealed clear separation between the microbial communities of pre-release and post-release C. chilia juveniles. This study demonstrated that VIE tagging was a suitable method for short-term marking of C. chilia juveniles. Lakeshores with water depths less than 300 cm were identified as preferred habitats for C. chilia juveniles. The primary adaptation period for cultured C. chilia juveniles released into the natural environment was found to be approximately 4–5 days. These findings contribute to our understanding of the post-release performance of cultured fish and may provide guidance for the management and evaluation of relevant stock enhancement programs.