Introduction. The study aims to explore the prevalence of heterophoria and associate factors in Tibetan grade-one students. Methods. The Lhasa Childhood Eye Study (LCES) is a school-based cohort study. 1942 grade-one students from 7 elementary schools were randomly sampled by stratified cluster sampling. Ocular examinations were performed in participants, including ocular motility, distance and near visual acuity, cycloplegic autorefraction, and stereoacuity. The near (33 cm) and distance (6 m) fixation cover test was used to differentiate orthophoria, heterophoria, and heterotropia, and the magnitude of the phoria was measured by the Maddox rod and prisma. Results. Of 1856 grade-one students completing all the ocular examinations, 1852 participants finished the ocular alignment test. The mean age was 6.82 ± 0.46 years (range 6∼10 years); 981 (52.97%) were males, and 871 (47.03%) were females. The prevalence of phoria was 22.89% (n = 424). At distance fixation, the prevalence of heterophoria, exophoria, and esophoria was 4.64%, 4.21%, and 0.43% separately, while at near fixation, the prevalence was 22.73%, 22.35%, and 0.38%. No vertical phoria was detected. The mean magnitude of heterophoria at near and distance fixation was −7.63 ± 5.15 PD (exo: −7.83 ± 4.91 PD, eso: +5.67 ± 3.61 PD) and −4.84 ± 5.94 PD (exo: −6.26 ± 4.20 PD, eso: +8.13 ± 3.04 PD). The prevalence of esophoria was associated with hyperopia (OR = 6.38, 95% CI: 1.15–35.28,
P
= 0.03; OR = 5.42, 95% CI: 1.04–28.24,
P
= 0.04) and amblyopia (OR = 16.02, 95% CI: 1.81∼141.96,
P
= 0.01; OR = 11.37, 95% CI: 1.34∼96.52,
P
= 0.03) at near and distance fixation. The prevalence of exophoria was associated with myopia at near fixation (OR = 2.43, 95% CI: 1.47–4.00,
P
<0.01). In the near heterophoria group, the proportion of children with abnormal stereoacuity was 23.26% (n = 97), significantly higher (χ2 = 5.70,
P
= 0.017) than that in orthophoria (17.99%, n = 244). Conclusions. In Lhasa, grade-one pupils have a lower prevalence of heterophoria. Near exophoria was associated with myopia, while esophoria was related to hyperopia and amblyopia both near and distance. Heterophoria may be one of the affected factors for reducing stereoacuity.