Objective: To explore the developmental characteristics of circadian rhythms in hypothalamus-pituitary-adrenal (HPA) axis during puberty. Methods: A total of 1 070 students from Grade 2-3 in 3 primary schools in Ma'anshan city, Anhui province, were selected for physical examination and circadian rhythm of HPA axis checked from 2015 to 2017. Saliva samples were collected at each of the following three time points: immediately upon wakening, 30 minutes after wakening and bedtime, with the index of circadian rhythm of HPA axis calculated, which including cortisol awake response (CAR), cortisol in puberty priming and diurnal cortisol slope (DCS). Testicular volume, palpation and visual inspection of breast development were used to assess the state of purbety development on boys and girls. Information on gender, date of birth, time to fall asleep, wake-up time and weekly physical activity were gathered through questionnaire survey. Non-parametric test was used to compare the differences of baseline, follow-up period and different adolescent developmental processes of each index on circadian rhythm of HPA axis. Results: During the period of follow-up program and comparing with the continuous undeveloped group, CAR and the changes of CAR showed significantly increase, both in the puberty priming group and continuous development group, with statistically significant differences (CAR: Z=8.551, 4.680, respectively; P<0.01; the changes of CAR: Z=4.079, 2.700, respectively, P<0.01). There were no significant differences noticed in CAR and the changes of CAR between puberty priming group or continuous development group. The area under the curve (AUC) of cortisol in puberty priming group was slightly higher than that in the persistent undeveloped group (Z=2.591, P=0.010). Both the changes of daily cortisol slope (DCS) in puberty priming group and continuing developed group decreased significantly, when comparing with those in continuous undeveloped group (Z=-2.450, Z=-2.151; all P<0.05). There was no significant difference noticed in the changes of cortisol in puberty priming and DCS between different puberty development stages (the changes of AUC: χ(2)=2.747, P=0.253; DCS: χ(2)=4.554, P=0.032). Conclusions: The indexes of circadian rhythm of HPA axis were associated with the development of puberty. Both the cortisol awakening response and the total amount of diurnal cortisol secretion showed an increase, along with the puberty development. The change of diurnal cortisol slope declined with the development of puberty.