Objectives: We previously reported a high prevalence of hypovitaminosis D (25OHD < 20 ng/mL) in Japanese pregnant women with threatened premature delivery. This study aimed to assess nutritional status and its relationship with bone-related markers and microarchitecture, as measured using quantitative ultrasonography (QUS), in Japanese women during the perinatal period. Methods: We recruited Japanese women who had just delivered at Fujita Health University Hospital (n = 103, cesarean/vaginal delivery = 50/53, age 33.9 ± 4.9 years). On the third day postpartum, their calcaneal QUS was measured, and fasting blood samples were collected. Results: The mean total energy intake (1720 ± 298 kcal/day) was lower than the normal range for Japanese women (2100 kcal/day). Their calcium intake (446 ± 130 mg/day) was significantly below the recommended daily intake (RDI) in Japan (660 mg/day), with 95% of participants consuming less than the RDI. Although the average vitamin D intake (8.7 ± 1.8 μg/day) met the Japanese RDI (8.5 μg/day), 36% of participants consumed less than the RDI. Calcium intake was positively associated with the intake of lipids, protein, and vitamins A, D, and K. Additionally, calcium intake but not vitamin D intake tended to correlate with serum 25-hydroxyvitamin D (25OHD) levels. The QUS indices showed no significant association with calcium or vitamin D intake. Conclusions: During the perinatal period, Japanese women had low calcium intake and relatively low vitamin D intake, accompanied by reduced 25OHD levels. These findings highlight the need for public health recommendations and policies to promote adequate calcium and vitamin D intake during pregnancy.