Although many online-based dietary surveys have been developed in recent years, systems that easily survey the dietary balance based on the Japanese diet are insufficient. This study aimed to evaluate the relationship between dietary balance scores from an online survey system based on the Japanese Food Guide Spinning Top, and nutrient/food intake calculated using the weighing method from dietary records (DRs), as well as to assess the system’s utility and applicability. An online dietary balance survey and semi-weighted DR assessment with food photographs were conducted in Japanese participants (n = 34). Registered dietitians entered the balance scores into the system based on the participants’ food photographs, and the scores were calculated using the system. Significant positive correlations (p < 0.001) were found between the online dietary balance scores and nutrient/food intake from DRs; especially for ‘grain dishes’ and carbohydrates (r = 0.704); ‘vegetable dishes’ and the vegetable dish group (sum of potatoes, vegetables, mushrooms, and algae) (r = 0.774); ‘main dishes’ and protein (r = 0.661); ‘milk’ and the milk and milk products group (r = 0.744); and ‘fruits’ and the fruits group (r = 0.748). Bland–Altman analysis showed that the dietary balance scores obtained by this system tended to underestimate the intake compared with the weighing method. Although there are limitations to the accurate estimation of nutrient and food intake, the online dietary balance scores obtained from the online dietary balance survey system were useful for understanding the dietary balance in the Japanese diet.