Purpose <p>Epidemiological studies using dietary biomarkers to investigate the association between whole grain intake and cardiometabolic health are lacking. We evaluate the 1-year longitudinal associations between urinary alkylresorcinol (AR) metabolites including 3-(3,5-dihydroxyphenyl)-1-propanoic acid (DHPPA) and 3,5-dihydroxybenozoic acid (DHBA), biomarkers of whole grain wheat and rye intakes, and cardiometabolic risk markers.</p> Methods <p>Total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), fasting blood glucose, systolic blood pressure (SBP) and diastolic blood pressure (DBP) were repeatedly measured at baseline and after 1-year in 482 Chinese community-dwelling adults. Blood lipids and fasting glucose were assayed by electrochemical luminescence method. We assessed makers of inflammation and insulin response at baseline. Brachial-ankle pulse wave velocity (baPWV) and ankle-brachial index (ABI) were measured after 1-year. We used linear models and linear mixed-effects models to analyze single measurement and repeated measurements, respectively.</p> Results <p>Each 1&#xa0;µg/g creatinine increase in urinary DHPPA concentrations was associated with a -0.72% (<i>P</i> = 0.027) and − 1.26% (<i>P</i> = 0.005) decrease in TC and LDL-C, respectively. Urinary DHPPA was also correlated inversely with interleukin 6 (β = -0.371, <i>P</i> = 0.018) and C-reactive protein (β = -0.487, <i>P</i> = 0.036) at baseline. Higher urinary DHBA levels were associated with lower levels of SBP and DBP, with the percentage differences per 1&#xa0;µg/g creatinine increment of -0.65% and − 0.74%, respectively (all <i>P</i> &lt; 0.05). No association was found between the urinary AR metabolites and arterial stiffness.</p> Conclusions <p>Our study suggests that high intakes of whole grain wheat and rye, reflected by urinary DHPPA and DHBA, are favorably associated with cardiometabolic risk markers.</p>