The environment of fish habitat has great effect on alter the composition of fish gut microbiome. However, It is still unknown how assembly process of the fish gut microbiota varies through changing habitat environment, especially for invasive tilapia, a species with strong adaptability to environmental changes. Here, we investigated gut microbiome of redbelly tilapia from three different habitat environment utilizing high-throughput 16S rRNA gene sequencing. Our findings showed that the gut microbiome of wild (high and low fragmented habitat) and pond-cultured redbelly tilapia were significantly different in terms of composition and diversity (alpha and beta). Further, stochastic processes acted as the primary regulator of the gut microbial community assembly of redbelly tilapia. When the habitat were altered from pond-cultured to wild environment, the contribution of undominated processes in the gut microbial community assembly declined, while the contribution of dispersal limitation increased. Co-occurrence network analysis indicated that habitat variation enhanced the gut microbial network complexity of invasive tilapia during the migration from pond to wild habitats. In addition, our findings indicated that the gut microbiome of wild tilapia possessed unique traits, including relatively high alpha diversity and a large relative proportion of genes coding for putative cellulolytic enzymes involved in the digestion of tilapia’s preferred food resource (hydrophytes), especially in the fragmented habitat with highly developed cascade dams. Our results also identified core biomarkers (Clostridium_sensu_stricto_1 and Bacillus) of gut bacterial community in wild redbelly tilapia, which provided beneficial knowledge of monitoring and managing invasive tilapia populations.