The purpose of this study was to describe the baseline refractive error, habitual accommodative tone (HAT) in Tibetan children and its longitudinal association with incident myopia and myopia progression.This was a prospective cohort study. From 7 elementary schools, 1440 children with mean age of 6.83 ± 0.46 years were included with full noncycloplegic and cycloplegic refraction data at baseline, 1-year and 2-year follow-up in the Lhasa Childhood Eye Study. Noncycloplegic and cycloplegic automated refraction were performed at baseline and annually over the next 2 years. HAT was measured as the difference in spherical equivalent (DSE) between noncycloplegic and cycloplegic refraction.The mean HAT decreased from a baseline value of 0.92 ± 0.82 diopters (D) to 0.55 ± 0.65 D, P < 0.0001 at 2 years. In multivariable logistic regression models, only baseline spherical equivalent (SE; P < 0.0001) was significantly (negatively) associated with 1- and 2-year incident myopia. Among 1386 children without myopia at baseline, 271 developed myopia over 2 years. For hyperopic children, baseline HAT was significantly associated with the incidence of myopia over 2 years (odds ratio [OR] = 0.43, P < 0.001), and the incidence of myopia was significantly lower with baseline HAT ≥0.5 D, compared to children <0.5 D. For 54 (3.75%) children who were myopic at baseline, SE was significant positively associated with myopic progression in univariable (P = 0.03) and multivariable general mixed linear regression analysis (P = 0.03).Baseline SE was an independent influencing factor for the incidence of myopia and its progression. The incidence of myopia was significantly higher with lower baseline HAT among hyperopic children, indicating that lower HAT was potentially associated with myopic development.