We aim to explore the independent associations of sedentary behaviors (SB) with body mass distribution among Chinese children. Data on the screen-based sedentary time (television viewing and computer use) and doing homework, physical activities and dietary intake of 1586 Chinese children (50.3% girls) aged 7–15 years were obtained through validated questionnaires. Skin-fold thickness, body height, and weight were measured to calculate percent body fat (%BF), fat mass index (FMI), and fat-free mass index (FFMI). Parental characteristics were collected by questionnaires. Among girls, time of SB (screen time or doing homework) was positively related to %BF, FMI, and FFMI (p < 0.03) after adjusting for maternal overweight, the average annual income of family, moderate-to-vigorous physical activity energy expenditure, and energy intake: Girls in the highest tertile of screen time/homework had 16.7%/23.3% higher relative FMI and 2.9%/2.9% higher relative FFMI than girls in the lowest tertile. Among boys, screen time was positively associated with FFMI (p < 0.003), but not related to %BF and FMI (p > 0.09), while time of doing homework was positively related to %BF and FMI (p = 0.03). Sedentary behaviors might be positively and independently related to fat mass among Chinese children, and were more pronounced in girls.