Oral health is composed of various oral health indices (OHIs), such as oral self-care habits, oral hygiene, oral function, and mastication ability. Oral self-care habits have frequently been examined for obesity risk. This study aimed to comprehensively clarify the association between OHIs and obesity risk. We collected data for 15 questions on the four OHIs and measured the body mass index of 3494 men and 2552 women aged 35–79 years. Obesity was defined as a body mass index ≥25 kg/m2. The four OHIs were scored by the corresponding questions (good as “reference”), and the summed score was defined as “comprehensive OHI”, that is, the fifth OHI. Each lowest tertile score was used as “reference”. Using multiple logistic regression analysis, odds ratios (ORs), 95% confidence intervals (CIs), and p-values for trends were estimated. In the men and women, the ORs were 1.37 (1.11–1.67, < 0.01) and 2.48 (1.80–3