Probiotics demonstrate the ability to maintain intestinal homeostasis and promote gut health. However, their effects on gut microbiota in adults over 60 years old with chronic metabolic disease (CMD) or cardio-cerebrovascular disease (CCD) remain poorly understood. This study analyzed 1586 stool samples from 1377 adults (CMD, CCD, and healthy controls) using 16S rRNA sequencing. Cohort 1 ( = 1168) was used for cross-sectional analysis, while cohort 2 ( = 209) underwent longitudinal assessment over approximately 13 months. The results demonstrated that probiotics promoted significant gut microbiota alterations across both cohorts. Probiotic supplementation significantly increased lactobacilli in the CMD, CCD, and H groups. In both cohorts, probiotic supplementation enhanced , sensu stricto 1, and in H groups, enhanced and in CMD groups, and reduced and in CCD groups. Notably, long-term supplementation not only elevated , group, and in all groups but also suppressed and in the CMD and CCD groups. Enterotype analysis revealed that probiotics increased the proportion of enterotype 1 and transition probabilities from enterotype 2 to 1 in the CMD and CCD groups, demonstrating that CCD/CMD gut microbiota exhibited greater responsiveness to probiotic modulation. Overall, this study suggests probiotics' role in modulating adult gut microbiota and their potential benefits in chronic metabolic and cardio-cerebrovascular diseases.