Abstract Purpose This research was designed to compare the effectiveness of repeated monochromatic low-level red-light (RMLRL) and 0.01% atropine in controlling myopia and axial elongation in myopic children. Methods We conducted a prospective, randomized, and single-blind controlled trial. A total of ninety-one children with myopia between the ages of 6 and 12 were selected for this study. These children had a cycloplegic spherical equivalent refraction (SER) ≥-5.00 D and ≤-0.75 D for each eye. The participants underwent random assignment in a 1:1 ratio between two experimental groups: the RMLRL group (n = 46, exposed to 650 nm red light passing through the pupil to the fundus, twice daily for 3 min with a minimum 4 h interval between each session) and 0.01% atropine group (n = 45, applied a single drop of 0.01% atropine bilaterally every night). The primary measured outcomes comprised alterations in SER and axial length (AL) after a duration of six months, while the secondary outcomes included changes in the subfoveal choroidal thickness(SFChT) and choroidal vessel volume (CVV). Results At the six-month follow-up, there were 45 children (97.8%) in the RMLRL group and 42 children (93.3%) in the 0.01% atropine group. The SER change was 0.24 ± 0.30 D compared to -0.29 ± 0.38 D (p < 0.001), and the change in AL was − 0.09 ± 0.14 mm compared to 0.15 ± 0.16 mm (p < 0.001) in the RMLRL and 0.01% atropine groups. The change in SFChT was 41.47 ± 34.27 um compared to 2.38 ± 16.69 µm (p < 0.001) in the RMLRL and 0.01% atropine groups. The CVV change was 0.01 ± 0.01 compared to 0.00 ± 0.01 (p < 0.001) in the corresponding two groups. No serious adverse events were reported in either the RMLRL or 0.01% atropine groups. Conclusions After six months of treatment, RMLRL had better effects than 0.01% atropine in preventing myopic progression and axial elongation among children with myopia in the central region of Mainland China.