Phthalates are well-known obesogens, but a few studies have explored their impacts on the childhood fat mass index (FMI), body shape index (ABSI) and body roundness index (BRI). Information from 2950 participants recruited in the Ma'anshan Birth Cohort was analyzed. The relationships between six maternal phthalate metabolites and their mixture and childhood FMI, ABSI and BRI were investigated. FMI, ABSI and BRI in children aged 3.5 y, 4.0 y, 4.5 y, 5.0 y, 5.5 y and 6.0 y were calculated. The latent class trajectory modeling categorized the FMI trajectories into “rapidly increasing FMI” (4.71%) and “stable FMI” (95.29%) groups; ABSI trajectories were categorized as “decreasing ABSI” (32.74%), “stable ABSI” (46.55%), “slowly increasing ABSI” (13.26%), “moderately increasing ABSI” (5.27%) and “rapidly increasing ABSI” (2.18%) groups; BRI trajectories were categorized as “increasing BRI” (2.82%), “stable BRI” (19.85%), and “decreasing BRI” (77.34%) groups. Prenatal MEP exposure was associated with repeated measurements of FMI (β = 0.111, 95% CI = 0.002–0.221), ABSI (β = 0.145, 95% CI = 0.023–0.268) and BRI (β = 0.046, 95% CI = −0.005–0.097). Compared with each stable trajectory group, prenatal MEP (OR = 0.650, 95% CI = 0.502–0.844) and MBP (OR = 0.717, 95% CI = 0.984–1.015) were linked to a decreased risk of “decreasing BRI” in children; there was a negative relationship between MBP and the “decreasing ABSI” group (OR = 0.667, 95% CI = 0.487–0.914), and MEP increased the risks of “slowly increasing ABSI” (OR = 1.668, 95% CI = 1.210–2.299) and “rapidly increasing ABSI” (OR = 2.522, 95% CI = 1.266–5.024) in children. Phthalate mixture during pregnancy showed significant relationships with all anthropometric indicator trajectories, with MEP and MBP always being of the largest importance. In conclusion, this study suggested that prenatal phthalate coexposure increased the childhood probability of being in higher ABSI and BRI trajectory groups. That is, children were more likely to be obese when they were exposed to higher levels of some phthalate metabolites and their mixture. The low-molecular weight phthalates, including MEP and MBP, contributed the greatest weights. Display omitted •The 1st study shows relations of prenatal PAEs with child ABSI and BRI trajectories.•Prenatal MEP exposure is associated with repeated measurements of FMI, ABSI and BRI.•PAE mixture increases the probability of being in higher ABSI and BRI trajectories.•MEP and MBP show largest weights for PAE mixture related to the adiposity trajectory.