This study aimed to investigate the changes in intestinal homeostasis and metabolism in mice after methamphetamine (MA) administration and exercise intervention. In this study, male C57BL/B6J mice were selected to establish a model of methamphetamine-induced addiction, and the gut microbiota composition, short-chain fatty acids (SCFAs), and amino acid levels were assessed by 16S rRNA, liquid chromatography–tandem mass spectrometry, and gas chromatography–tandem mass spectrometry, respectively. The results showed that 23 dominant microbiota, 12 amino acids, and 1 SCFA were remarkably higher and 9 amino acids and 6 SCFAs were remarkably lower in the exercise model group than in the control group. Among the top 10 markers with opposite trends between the exercise intervention group and model group, the differential microbiomes included Oscillibacter, Alloprevotella, Colidextribacter, Faecalibaculum, Uncultured, Muribaculaceae, and Negativibacillus; amino acids included proline; and SCFAs included isovaleric acid and pentanoic acid. Proline was negatively correlated with Negativibacillus and positively correlated with pentanoic acid. The results suggested that moderate-intensity aerobic exercise may modulate changes in the composition of the gut microbiota and the levels of amino acids and SCFAs induced by MA administration.