The study aimed to explore the associations between water intake and body composition, and to investigate the differences of body composition among young male athletes. A cross-sectional study was conducted among 111 young male athletes in Beijing, China. Total drinking fluids (TDF) and water from food were assessed by a 7-day, 24-hour fluid intake record questionnaire and duplicate portion method, respectively. The osmolality of 24-hour urine and blood samples were tested. The body composition was tested with a bioelectrical impedance analyzer (BIA) twice at 5 minutes interval. According to the recommendations of total water intake (TWI) and TDF of China, participants were divided into two groups, respectively. Participants were divided into three groups according to 24h urine osmolality. Pearson’s correlation coefficients were performed to determine the relationship between water intake and body composition. Chi-square tests and Students’ t tests were used to compare the differences. A total of 109 subjects completed the study. TDF and TWI were positively correlated with total body water (TBW), intracellular water (ICW) and extracellular water (ECW), respectively (r=0.230, p=0.016; r=0.234, p=0.014; r=0.242, p=0.011; r=0.275, p=0.004; r=0.243, p=0.011; r=0.243, p=0.011). The TBW/BW was positively associated with TDF percentage of body weight (TDF/W), water from food percentage of body weight and TWI percentage of body weight (TWI/W), respectively (r=0.267, p=0.005; r=0.217, p=0.024; r=0.316, p=0.001). Participants achieved the recommendation of TDF of China had 1.3kg, 0.9kg, 0.5% higher skeletal muscle mass (SMM), ICW and TBW/BW than those who did not, respectively (all p < 0.05); with the FFM and TBW tended higher (p=0.051; p=0.050). Those met the recommendation of TWI of China had 1.3kg, 2.4 kg, 1.1 kg, 0.6kg and 1.7kg higher SMM, free fat mass (FFM), ICW, ECW and TBW than their counterparts, respectively (all p < 0.05). There were no significant differences in values of body composition among subjects in different hydration groups (all p> 0.05). Moderate associations were found between water intake and body composition. Participants met the recommendation of TWI or TDF had better distribution of body composition than their counterparts. Habitual water intake affected the body composition among athletes in free-living conditions.