Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder characterized by reproductive and metabolic abnormality disorders. Dietary factors influence the body composition and hydration status, which may exacerbate PCOS symptoms. The aim of this study was to assess the associations between the habitual nutrient intake and bioelectrical impedance analysis parameters in Polish women with PCOS and healthy controls, in order to identify potential nutritional targets for a non-pharmacological intervention. Methods: This study involved 50 women aged 18–45 years (25 with PCOS and 25 healthy). Participants kept 7-day food diaries and their body composition was assessed using the SECA mBCA 515 analyzer. The nutrient intake was compared with EFSA recommendations. Results: Women with PCOS had a higher body weight, waist circumference and body mass index, visceral adipose tissue, and fat mass index, despite no difference in their total energy intake. They consumed more omega-3 fatty acids (EPA + DHA) than the control group. Vitamin D deficiency and irregular supplementation were common in both groups. Body composition parameters such as the phase angle and ECW/TBW ratio correlated with the diet quality—especially with protein; fiber; and vitamin B2, B12, and folate levels. Conclusions: The obtained results showed significant differences in body compositions and the presence of a relationship between the nutrient intake and bioimpedance parameters in women with PCOS. These results emphasize the importance of a comprehensive nutritional and body composition assessment in planning dietary interventions in this group of patients.