A prospective community-based cohort study was conducted to investigate the effects of obesity on hyperhomocysteinemia (HHcy) in community residents from Shanghai, China, with a median follow-up period of 2.98 years. The exposures were high body mass index (BMI) (BMI ≥ 28.0 kg/m2) and high waist circumference (WC) (WC ≥ 85.0 cm for female and WC ≥ 90.0 for male) at baseline investigation, and the outcome was the incident of HHcy after the follow-up. A restricted cubic spline (RCS) was performed to assess the possible nonlinear relationship of BMI and WC with HHcy. A Cox proportional hazard regression model was used to evaluate the association between BMI and WC measured obesity and the risk of HHcy (Hcy level > 15 µmol/L). No significant non-linearity was found between BMI and WC with HHcy. Cox regression model showed that underweight measured by BMI was negatively associated with the risk of HHcy after controlling for confounder variables (adjusted HR = 0.64, 95% CI = 0.42 to 0.99). While abdominal obesity was positively associated with the risk of HHcy for those without CVD-related comorbidities (adjusted HR = 1.26, 95% CI = 1.05 to 1.51). Our results suggested that individuals could maintain a relatively low BMI and normal WC to lower the risk of HHcy.