Evidence suggests that excessive screen time in early childhood is related to children’s physical and mental health. This study aimed to review the relationships between screen media use and several health indicators in infants, toddlers, and preschoolers. A systematic search was conducted by two independent reviewers on PubMed, Web of Science, Embase, and Cochrane Library to identify the eligible studies, with an end date of 13 August 2019. Included studies (published in English) were peer-reviewed and met the determinate population (children aged 0–7 years with screen media exposure and related health outcomes). The AHRQ, NOS, and the Cochrane Handbook were used to evaluate the cross-sectional study, cohort study, and RCT, respectively. A meta-analysis and narrative syntheses were employed separately. Eighty studies (23 studies for meta-analysis) met the inclusion criteria for the systematic review. Strong evidence of the meta-analysis suggested that excessive screen time was associated with overweight/obesity and shorter sleep duration among toddlers and preschoolers. Excessive screen use was associated with various health indicators in physical, behavioral, and psychosocial aspects. Better-quality research on newer media devices, on various kinds of contents in young children, and on dose–response relationships between excessive screen use and health indicators are needed to update recommendations of screen use.