Reducing visceral fat is an important issue for obesity prevention. We previously reported a novel dietary intervention program using “Optimized Nutri-Dense Meals” based on the nutrients described in Dietary Reference Intakes in Japan. This open-label randomized controlled trial evaluated the visceral fat reducing effect of the program. In total, 100 Japanese obese/overweight male patients were recruited and divided into a control group that continued their usual diets and a test group that consumed test meals twice per weekday for four weeks. Visceral fat area, set as the primary outcome, was significantly decreased in the test group compared with the control group. Regarding other outcomes, the occupancy levels of some gut floras and presenteeism scores were significantly increased in the test group compared with the control group. These results indicate that dietary intervention based on the Dietary Reference Intakes can prevent visceral fat accumulation and contribute to the improvement of health, without the need for completely replacing the everyday diet.