Objective To compare the effect of atropine drug penalization and patching therapies of children with anisometropic amblyopia or strabismus amblyopia. Methods In this prospective clinical study, children and adolescents diagnosed with anisometropic amblyopia or strabismus amblyopia who had complete clinical data of more than 12 months were recruited from January 2013 to March 2015. They were divided into an atropine penalization group and patching group. And patients were further divided into mild, moderate, severe degree to analyze. The degree of amblyopia for the two groups was compared with the Wilcoxon rank sum test. The effective rate and cure rate for the two groups were compared by chi-square tests. Results A total of 85 patients (85 eyes) with anisometropic or strabismus amblyopia were recruited and divided into a patching group of 52 patients (52 eyes) and an atropine penalization group of 33 patients (33 eyes). The cure rates were 60% and 64% in the patching and penalization groups respectively (χ²=0.137, P=0.711). The effective rates were 88% and 85% for the patching and penalization groups respectively (χ²=0.234, P=0.629). There was also no significant difference between the two groups when the rates of effectiveness for different degrees of amblyopia were compared. Fifty-two eyes in the patching group and 29 eyes in the penalization group developed a fixating eye after 3-6 months of treatment, but 4 eyes in the penalization group did not develop a fixating eye. Conclusion Atropine drug penalization therapy has a similar effect on anisometropic or strabismus amblyopia in children as does traditional patching therapy.