Background <p>The aim of this study was to investigate the effectiveness of 0.01% topical atropine (ATR) on myopic prevention in a population with different low refractive errors.</p> Methods <p>A retrospective cohort study was conducted on children with low refractive error. They were classified according to the application of 0.01% ATR, and 55 and 67 eyes constituted the ATR and non-ATR groups, respectively. The primary outcomes were changes in spherical equivalent refraction (SER) and axial length (AXL) after a one-year interval. Statistical analysis was carried out using the independent T test and generalized linear model.</p> Results <p>The SER change and AXL elongation were significantly lower in the ATR group compared to the non-ATR group (<i>P</i> &lt; 0.001 for both). For different initial SERs, SER and AXL progression in the individuals with plus initial SER were significantly lower than those with minus initial SER after ATR treatment (both <i>P</i> &lt; 0.05). High outdoor activity was inversely correlated with myopic progression in the ATR group (<i>P</i> = 0.006). For the non-ATR population, young initial age, minus initial SER, and high near-work activity were related to myopic progression, while high solar exposure and high outdoor activity were inversely correlated with the development of myopic progression (all <i>P</i> &lt; 0.05).</p> Conclusions <p>Application of 0.01% ATR might relates to myopic prevention effect in a population with low refractive error, especially for plus initial SER.</p>