Background: The Korean Obesity Index, which contains standard reference data (SRD) of obesity, was established in 2016 and revised in 2017 based on national health screening data to provide the distribution of the body mass index (BMI) of the whole population of Korea as a reference. This study aimed to investigate the effect of the SRD of obesity on the incidence of hypertension (HTN) and diabetes mellitus (DM). Methods: The percentile of BMI was calculated for each of the 864 subgroups by defined by gender, region, and age group according to the groupings in the SRD. Incident cases were defined as the presence of HTN and DM and medication prescription in the health care utilization database for a given individual in 2017, but not in 2015-2016. Logistic regression for the incidence of HTN and DM according to the relative distribution of BMI was performed. Gender, age, insurance type, insurance contribution, smoking, drinking, physical activity, blood pressure, waist circumference, fasting glucose, triglycerides, high-density lipoprotein cholesterol, the Charlson comorbidity index (2012-2014), and diagnosis and medication for HTN and DM (2015-2017) were adjusted in the analysis. Results: The C-statistics of the fully adjusted model for HTN and DM were 0.799 and 0.852, respectively. The risks of HTN and DM increased by 1.007 and 1.011 times, respectively, for each 1-percentile increase in BMI. Conclusion: The results showed that BMI was associated with the incidence of HTN and DM according to the SRD. The relative distribution of BMI can be used to motivate self-care through providing more detailed information to individuals.