Background Relative peripheral refraction (RPR) is a significant factor that participates in myopic development. Here, we evaluated the effects of atropine 0.01% eyedrops, as an antimyopia drug, on RPR. Methods Seventy-three children were enrolled from a randomized, double-blinded, placebo-0.01% atropine eyedrops cross-over trial. The study group had used the placebo for one year and then crossed over to atropine 0.01% eyedrops for half a year. The control group had used 0.01% atropine for one year and then crossed over to placebo eyedrops for half a year. Central and horizontal peripheral refractions (15 degrees and 30 degrees at the temporal and nasal retina) were measured under non-cycloplegia and cycloplegia. Results No significant differences in age, gender, and central refraction were identified between the two groups (P > 0.05). Under non-cycloplegia, the control group showed significant relative hyperopia in the temporal 30 degrees retina and the nasal retina (P = 0.031; P < 0.001; P < 0.001). In the study group, the relative hyperopia in the temporal 30 degrees retina disappeared (P = 0.983). After cycloplegia, the control group had less myopia in central refractions and less hyperopia in temporal RPR (P < 0.001; P = 0.039; P < 0.001). The study group did not present significant changes in central refractions and temporal RPR (P = 0.122; P = 0.222; P = 0.475). Conclusions For myopic children, atropine 0.01% eyedrops can alleviate relative hyperopia in the temporal retina and the hyperopic shift before cycloplegia. The effect might participate in myopia control.