Aim To investigate the effects of the traditional Chinese exercise Baduanjin on gut microbiota and metabolomic profiles of patients with chronic heart failure, elucidating its potential therapeutic benefits by characterizing microbiome and metabolomic features. Methods Thirty-two patients with chronic heart failure were enrolled and divided into two groups:the control group received conventional treatment, while the Baduanjin group practiced Baduanjin in addition to conventional therapy. After 12 weeks of intervention, fecal and serum samples were collected from both groups of patients for gut microbiota and serum metabolomics analysis. Results At baseline, Baduanjin group and control group showed no significant differences in demographic characteristics, vital signs, heart failure classification, or comorbidities (P＞0.05). After 12 weeks of Baduanjin exercise, compared with the control group, the Baduanjin group showed a significant increase in the 6-minute walking distance (P＝0.026); meanwhile, the improvement in peak oxygen uptake exceeded the minimum clinically significant difference, but the intergroup difference did not reach statistical significance (P＝0.323). Analysis of gut microbiota showed that compared with the control group, the Baduanjin group had relatively higher alpha diversity, but there was no statistically significant difference in alpha diversity and beta diversity between the two groups (P＞0.05); 14 discriminative taxa were identified (7 related to the Baduanjin group and 7 related to the control group), at the genus level, the relative abundance of the Dialister was highest in the Baduanjin group (P＝0.021), while the relative abundance of the Haemophilus was highest in the control group (P＝0.037). Metabolite profile analysis showed that non-targeted metabolomics results indicated that the metabolite profile characteristics of the two groups were distinguishable; 39 differential metabolites were identified, with enriched pathways including cancer-related choline metabolism, primary bile acid biosynthesis, glycerophospholipid metabolism, and niacin/nicotinamide metabolism. The analysis of gut microbiota combined with serum metabolites showed a positive correlation between the genus Dialister and lysophosphatidylcholine (20∶1(11Z)/0∶0) in the Baduanjin group (r＝0.55, P＝0.001), and there was a positive correlation between Haemophilus and N1-methyl-2-pyridone-5-carboxamide in the control group (r＝0.56, P＝0.001). Conclusion Baduanjin exercise can improve exercise endurance in patients with chronic heart failure, and may also improve the intestinal metabolic environment and skeletal muscle mitochondrial energy metabolism by increasing the production of short chain fatty acid related bacteria and raising the level of lysophosphatidylcholine.