This study aimed to analyze the impact of single nucleotide polymorphism (SNP) of ADCY3 (encoding adenylate cyclase 3) on the outcome of high-intensity interval training (HIIT) on body composition and screen genetic markers sensitive to HIIT in Chinese Han youth. A total of 237 non-regular exercise Han college students were recruited in a 12-week HIIT program, attending sessions 3 times a week. Before and after the HIIT program, their body composition was measured. DNA from the white blood cells was extracted and genotyped. PLINK (V1.09) software was used for quality control screening of SNPs loci, and a linear regression model was constructed to analyze the association between ADCY3 gene SNPs loci and body composition. ANOVA multiple comparisons (LSD) were performed to test the difference between groups, with the significance level set at 0.05. The results showed that: 1) A total of 22 SNPs loci were identified by the gene microarray scanning of ADCY3 gene, with 15 of them meeting the quality control criteria. The rs6753096 locus was associated with the training effect of HIIT on body composition; 2) The rs6753096 locus was not associated with pre-HIIT body composition; 3) Compared with volunteers with TT genotype, those with CT/CC genotype exhibited significant decrease in body mass index (BMI) and total body fat after training (P < 0.05); Male volunteers carrying the C allele had more significant training changes in skeletal muscle and lean body weight, while HIIT was more effective in decreasing body fat in female volunteers with CT/CC genotype; 4) The rs6753096 locus was significantly correlated with body fat sensitivity to HIIT (P = 0.0475), indicating that volunteers with CT/CC genotype were more sensitive to HIIT. In conclusion, 12-week HIIT program effectively improved the body composition of college students. The ADCY3 gene rs6753096 locus is not associated with pre-HIIT body composition, but it is associated with body composition sensitivity to HIIT, with individuals carrying CT/CC genotype showing greater responsiveness to HIIT.