Background: Levels of pentraxin 3 (PTX3), an anti-inflammatory cardioprotective protein, increase after weight loss in obese men and aerobic exercise in non-obese adults. However, the effect of nutritional characteristics on PTX3 levels remains unclear. This population-based, cross-sectional study investigated the association between circulating PTX3 levels and food intake in Japanese adults. Methods: We hypothesized that the consumption of high amounts of high-sugar foods would lead to low plasma PTX3 levels, resulting in obesity. This study included 327 participants categorized depending on the consumption of the recommended amount of confectionary and sugar-sweetened beverages (CSSB) into high and low groups.Results: PTX3 levels were significantly lower in the high CSSB group than in the low CSSB group. Biological sex was the strongest effector of PTX3 levels. Moreover, the intake of Tsukudani and CSSB, as well as some metabolic syndrome factors, also affect PTX3 levels. In the groups categorized by sex and age, the determinants of PTX3 levels differed. Body mass index, waist circumference (WC), and high-density lipoprotein cholesterol (HDL-C) were significantly associated with PTX3 levels in women. Tsukudani, HDL-C, heart rate, saturated fatty acids, systolic blood pressure, and CSSB were associated with PTX3 levels in individuals aged >65 years. Conclusion: Our results show that circulating PTX3 levels are affected by sex, sugar-rich foods, and metabolic syndrome characteristics (WC, HDL-C).