Abstract: It is important to study the differences of intestinal flora and fish flavor quality of Cyprinus carpio var. Jinbei under different culture modes for its breeding optimization. We applied illumina high-throughput sequencing technology to analyze intestinal microflora of C. carpio var. Jinbei cultured in paddy fields (FGF) and ponds (FGP), respectively. Besides, we used liquid chromatography (LC) to determine the flavor substances, and used headspace solid phase microextraction combining with gas chromatography-ion mobility spectrometry (HS-SPME-GC-IMS) to determine the volatile flavor substances. Then we calculated the taste activity value and relative odor activity by combining the sensory threshold. Significant difference analysis shows that Vibrio, Bacteroides, Alteromonadales, Shewanella, Pseudomonas psychrophila and Brevinema were the main bacteria in FGF group, while Moraxella and Klebsiella were the main bacteria in FGP group. The contents of IMP and flavor activity in FGF group (1.676 g·kg⁻¹ and 6.705) were significantly higher than those in FGP group (0.246 g·kg⁻¹ and 0.985). The contents of umami amino acids and sweet amino acids in FGF group (0.143 and 2.052 g·kg⁻¹) were higher than those in FGP group (0.109 and 2.001 g·kg⁻¹). However, the contents of bitter amino acids in FGF group (3.193 g·kg⁻¹) were lower than those in FGP group (3.836 g·kg⁻¹). Moreover, the components of volatile compounds were complex, and the types of key odor compounds (ROAV≥1) and compounds that could modify the overall flavor (0.1≤ROAV<1) were different. The correlation analysis between bacteria genera and flavor substances shows that Vibrio, Bacteroides, Klebsiella and Morganella were significantly correlated with flavor substances (0.01≤P<0.05 & 0.001≤P<0.01 & P<0.001). The results indicate that cultivation mode affects the intestinal microbes of fish, and affects the flavor quality of fish indirectly.