To evaluate the effect of 0.01% atropine eye drops on the ocular surface in children for the control of myopia. Methods: A total of 72 participants were recruited for this prospective study. Prior to and after 1, 3, and 6 months of 0.01% atropine administration, an ocular surface disease index (OSDI) questionnaire was obtained, Keratograph 5M was used for the measurement of the tear meniscus height (TMH), noninvasive keratographic tear film break-up time (NK-BUT, the first keratographic break-up time, [NK-BUT first ] and the average keratographic break-up time, [NK-BUT ave ]), bulbar redness (BR), meiboscore (MS), and anterior segment optical coherence tomography (AS-OCT) was used to calculate the inferior tear meniscus area (TMA). Results: After using the 0.01% atropine eye drops for 1 month, 9 subjects complained of discomfort immediately after administration, but this quickly subsided, and 1 subject was temporarily dazzled. All the ocular surface symptoms were mild and occurred rarely. After 3 months, these complaints no longer occurred. Compared with the baseline values, the OSDI scores (0.08 ± 0.28), values of TMH (0.23 ± 0.04 mm), TMA (0.0420 ± 0.0444 mm 2), NK-BUT first (9.39 ± 5.25 s), NK-BUT ave (10.49 ± 4.94 s), BR (0.63 ± 0.37), and MS (0.89 ± 0.70) did not change significantly after 6 months of 0.01% atropine eye drop administration (P > 0.05). Conclusion: In this 6-month prospective study, no side effects were observed on the ocular surface after using 0.01% atropine in children.