Obesity has become a major risk factor for the development of chronic diseases such as insulin resistance, type 2 diabetes mellitus, and cardiovascular disease. Moreover, obesity induces chronic inflammation in adipose tissue, liver, skeletal muscle, and the vascular system. Quercetin is the major representative of the flavonoid subclass of flavonols, which is ubiquitously contained within natural plants such as green tea, and vegetables, including onions and apples. Researchers have focused greater attention to the beneficial physiological roles of quercetin, which has anti-oxidative, anti-inflammatory, and anti-fibrotic effects on insulin resistance and atherosclerosis in obesity-related diseases. Also, the anti-inflammatory effects of quercetin on intestinal microbiota have been demonstrated in obesity. In addition, there is increasing evidence that quercetin is associated with epigenetic activities in cancer, and in maternal undernutrition during gestation and lactation. In this review, we focus on the chemical properties of quercetin, its dietary sources in obesity, and its anti-inflammatory effects on insulin resistance, atherosclerosis, intestinal microbiota, and maternal under-nutrition with epigenetic activity.