The childhood high body mass index (BMI) is associated with cardiovascular risk, but the association between childhood BMI trajectory patterns and cardiovascular risk remains unclear. The purposes of this study are to identify subgroups of individuals with similar trajectories in BMI during childhood, and to determine the relationship of childhood BMI trajectories with subclinical cardiovascular disease in young adulthood, indexed by intima-media thickness (IMT) and left ventricular mass index (LVMI). The participants were from the Georgia Stress and Heart (GSH) study. A total of 626 participants with BMI measured 3–12 times during childhood (5–18 years old) were included. By using latent class models, three trajectory groups in BMI were identified, including high increasing (HI), moderate increasing (MI) and normal group. We found that childhood trajectory of BMI was significantly associated with IMT and LVMI in young adulthood even after adjustment for BMI in young adulthood. Our results suggested that different BMI trajectory patterns exist during childhood. We for the first time reported the association between childhood BMI trajectory patterns and subclinical cardiovascular risk in young adulthood, indicating that monitoring trajectories of BMI from childhood may help to identify a high cardiovascular risk population in early life.