Aims: Epidemiological studies that use dietary biomarkers to investigate the association between whole grain intake and the risk of obesity are sparse. We assessed the association between urinary alkylresorcinol metabolites including 3-(3,5-dihydroxyphenyl)-1-propanoic acid (DHPPA) and 3,5-dihydroxybenzoic acid (DHBA), biomarkers of whole grain wheat and rye intake, and body fat measures. Methods: We measured urinary excretion of DHPPA and DHBA, body weight, height, and circumferences of the waist and hip at the baseline and again after 1-year in a representative sample of 306 community-dwelling adults in Huoshan, China. We also measured liver fat accumulation [indicated by the controlled attenuation parameter (CAP)] and other body composition after 1 year. Multivariate-adjusted linear models and linear mixed-effects models were used to analyze single measurement and repeated measurements, respectively. Results: Each 1 μg g-1 creatinine increase in urinary DHPPA levels was associated with 0.21%, 0.23%, 3.64%, and 4.80% decrease in body weight, body mass index (BMI), body fat mass (BFM) and visceral fat level (VFL), respectively (all P < 0.05). Higher DHBA levels were inversely associated with CAP (percentage difference per 1 μg g-1 creatinine increment: -1.98%, P < 0.05). Higher total urinary alkylresorcinol metabolite (DHPPA + DHBA) levels were associated with lower body weight, BMI, BFM, VFL, and CAP, with the percentage differences per 1 μg g-1 creatinine increment of -0.27%, -0.27%, -3.79%, -5.12%, and -2.24%, respectively (all P < 0.05). Conclusions: Our findings suggest that the intake of whole grain wheat and rye, reflected by urinary DHPPA and DHBA, is favorably associated with liver fat and other fat measures.