We aimed to determine the prevalence and possible ethnic variations in strabismus and amblyopia among multiethnic school-aged children in rural China. A total of 9,263 children (4,347 Han, 3,352 Yi, 799 Dai and 765 Bai) aged 6 to 14 years were analyzed. Comprehensive eye examinations including monocular distance visual acuity, anterior segment examination, autorefraction, cover testing and ocular motility were conducted. Manifested strabismus was detected in 3.53% of the overall population. The prevalence of strabismus was 3.29% in Han, 4.12% in Yi, 2.25% in Dai, and 3.66% in Bai ethnic groups with marginally inter-ethnic differences (P = 0.046). There was an increasing trend in the prevalence of strabismus with increasing age (P < 0.001). Amblyopia affected 132 children (1.43%) overall, with no statistical differences in gender and age. The prevalence of amblyopia was highest in Dai ethnic group (2.00%) and lowest in ethnic Yi ethnic group (1.04%) with no significant difference being detected (P = 0.062). Refractive error and strabismus were the two major factors associated with amblyopia. No significant ethnic differences in strabismus and amblyopia among Chinese ethnic minorities were observed. Refractive error and strabismus were the major causes for amblyopia in rural Chinese children.