Maternal underweight and inadequate gestational weight gain (GWG) are problems in Japan. However, increases in food intake aimed at weight gain alone are not sufficient for mother-child health. This study assessed diet quality based on the 3-day dietary records of pregnant women in an urban area of Japan in order to show the importance of evaluating diet quality, using the Nutrient-Rich Food Index 9.3 (NRF9.3), which is one metric based on nutrition profiling, and the Japanese Food Guide Spinning Top (JFGST). After excluding misreporters of energy intake, we stratified women (n = 91) by pre-pregnancy body mass index (BMI) and determined energy intake, diet quality status, and their relationship with GWG. Intakes of carbohydrate-containing staple foods, vegetable dishes, and fruit were insufficient regardless of BMI. Most of the underweight women with inadequate GWG had insufficient energy intake but high diet quality, as assessed by NRF9.3. In contrast, most women who consumed energy within the recommended range had low diet quality and gained weight at inappropriate levels. These results highlight the importance for pregnant Japanese women to maintain diet quality through a nutrient-dense diet, while simultaneously increasing energy intake after evaluation of their individual diet quality.