Objective: To examine pubertal timing across body mass index (BMI) trajectory under polygenic susceptibility in boys and girls,and to provide a reference basis for children’s adolescent development deviation form early intervention strategies. Methods: All the participants were recruited from 1 to 3 grade in 2016 from 2 Bengbu primary school and were followed up for 3 consecutive years. The study comprised 997 children (418 boys) with available data for height, weight, BMI, breast Tanner stages and testicular volume annually. The polygenic risk score (PRS) was computed based on 17 SNPs derived from published genome-wide association studies for early pubertal timing. Group-based trajectory model (GBTM) was used to identified BMI trajectory in children. Accelerated failure time model (AFT) was used to examine associations of different BMI trajectory and polygenic risk with pubertal development in boys and girls. Results: Classes of BMI trajectory were persistently healthy weight, persistently overweight and persistently obesity. Adjusted concomitant variables, boys with persistently obesity exhibited 6.10-mo delay of testicular volume in low polygenic risk group (adjusted TR=1.05，P=0.04). Compared with the girls in persistently healthy weight group, the girls with low PRS were persistently overweight or obesity, which was associated with thelarche age 3.42 and 6.84-mo earlier, respectively (adjusted TR=0.97，0.94,P<0.01). Persistently overweight or obesity in girls with moderate PRS was associated with an earlier age of thelarche timing of 6.72 and 8.96-mo, respectively (adjusted TR=0.94，0.92, P<0.01). At high PRS groups, the persistently obese girls were found to have a more advanced age (10.80 and 12.96-mo, respectively) of thelarche (adjusted TR=0.90，0.88, P<0.01). Conclusion Persistently overweight and obesity is associated with early thelarche in girls, but persistently obesity may increase delayed puberty risk in boys with low polygenic risk.