Phenylalanine hydroxylase (PAH) deficiency leads to phenylalanine accumulation and results in phenylketonuria (PKU). Phenylketonuria can contribute to severe inability such as mental impairment. Early diagnosis and dietary intervention can have beneficial effects on maintaining normal neural and cognitive function in patients with PKU. However, a long-term low phenylalanine diet may put children at risk of malnutrition. A food supplement was therefore used for children with PKU under dietician supervision according to dietary reference intakes (DRIs). In this cross-sectional study, we enrolled patients with PKU and age-matched controls to compare their anthropometry data [weight, height, body mass index (BMI), and body composition using bioelectrical impedance analysis (BIA)], and correlated it with their dietary intake based on 24-h dietary recall. For continuous parameters, the data were expressed as median ± standard deviation (SD), and the Mann-Whitney U test was used to test the difference among the groups. Correlation by natural proteins, body fat, and fat-free mass were evaluated using the Pearson correlation coefficient. Twenty-two participants diagnosed with PKU (ages 8-27 years; mean 15.23 ± 5.23) and a control group of 22 non-PKU participants (ages 8-39 years; mean 19.73 ± 10.6) were recruited for this study. Between the two groups of participants, no significant difference was found in height, weight, BMI, muscle mass, or fat mass. The percentage of natural protein has no effect on body composition. We found a significant positive correlation between the total protein intake percentage of DRIs and muscle mass (r = 0.491, p = 0.020) and a significant negative correlation in the total protein intake percentage of DRIs and fat mass (r = -0.475, p = 0.025) in participants with PKU. There were no significant differences in body composition and nutrition intake between patients with PKU (under metabolic control) and healthy subjects. Thus, giving proper nutrition treatment may have beneficial effects on body growth and nutrition status in patients with PKU in Taiwan.