Objective To investigate the early factors affecting different outcomes of children with congenital hypothyroidism (CH). Methods A total of 80 children with CH screened and diagnosed at Meizhou Maternal and Child Health Care and Family Planning Service Center between December 2013 and March 2017, who were treated with levothyroxine sodium for 2~3 years and then discontinued for assessment and followed up for over 1 year, were selected and divided into the permanent CH group (29 cases) and transient CH group (51 cases) according to disease outcomes. The clinical conditions of the children were retrospectively analysed to seek early factors affecting outcome. Results The initial screening thyroid hormone values [ 63.89 (43.89, 114.25) vs 38.54 (27.27, 60.00) mIU/L ], the required dose to restore normal thyroid hormone in permanent and transient CH group [(4.29±1.46) vs (3.38±1.34) μg/(kg·d)], and the proportion of early normal thyroid ultrasound [58.6% (17/29) vs 90.2% (46/51)] had significant differences(P<0.05). The initial screening thyroid hormone value (optimal threshold: 37.825 mIU/L, AUC=0.745, sensitivity 0.897 and specificity 0.490) and the levothyroxine sodium dosage at eighth month of age [optimal threshold 3.38 μg/(kg·d), AUC=0.759, sensitivity 0.586 and specificity 0.843] could early distinguish permanent and transient CH children. Conclusions Initial screening thyroid hormone values and postnatal levothyroxine sodium dosage had an early predictive effect on clinical outcome in children with CH.