In a previous study, we found that higher waist circumference (WC) and higher body mass index (BMI) both increase the risk of chronic spontaneous urticaria (CSU). The aim of this study was to determine whether WC and BMI also increase the duration of CSU. We used multivariable Cox proportional hazards models to determine the hazard ratio (HR) for longer disease duration (longer than 3 years) according to WC and BMI. A total of 52,667 subjects were enrolled and their mean age was 54.5. After adjustments for other confounding variables the high WC/high BMI group had 1.062 times higher HR (95% CI, 1.028–1.098) than the normal WC/normal BMI group. Interestingly, the high WC/normal BMI group showed a significantly higher HR (1.053; 95% CI, 1.008–1.101) than the normal WC/normal BMI group, but not the normal WC/high BMI group (0.998; 95% CI, 0.951–1.046). Taken together, our results suggest that high WC rather than high BMI is a predictive risk factor for the longer disease duration of CSU.