Objective To observe the effects of initial doses and treatment timing of levothyroxine (L-T4) on the clinical effcacy in children with congenital hypothyroidism (CH). Methods This study included 98 children who had an abnormal level of thyroid stimulating hormone (TSH) in neonatal screening in four regions of Yunnan Province and who fnally had a confrmed diagnosis of CH. They received treatment with L-T4 and were divided into standard dose group (10-15 μg/kg per day) and low dose group ( < 10 μg/kg per day) by the therapeutic dose of L-T4. Meanwhile, these patients were also classifed into two treatment groups based on the starting time of L-T4 treatment, namely under 2 months old group and more than 2 months old group. The thyroid function and physical and neural development were examined before and after treatment. Results Compared with the low dose group, the standard dose group had a signifcantly lower TSH level and a signifcantly higher free thyroxine (FT4) level at 2 weeks after treatment (P < 0.05). There were no signifcant differences in TSH and FT4 levels at other time points after treatment between the standard and low dose groups (P > 0.05). The physical and neural development were not signifcantly different between the two dose groups before and at all time points after treatment (P > 0.05). At all time points after treatment, the levels of TSH and FT4 and physical development were not signifcantly different between the different starting time groups (P > 0.05). However, the Gesell score was signifcantly higher in the under 2 months old group than in the more than 2 months old group at all time points after treatment (P < 0.05). Conclusions The standard dose group has a better treatment outcome than the low dose group, whereas the symptoms of hyperthyroidism deserve close attention. The treatment timing is vital to the neurodevelopment of children with CH. Once diagnosed, the patients should receive treatments immediately.