To evaluate the 1-year effects of orthokeratology (OK) lenses and spectacle lenses with highly aspherical lenslets (HALs) on axial length (AL) elongation in children with unilateral myopic anisometropia. This ambispective cohort study recruited 81 children aged 8-14 years with unilateral myopic anisometropia. Of these, 42 participants (mean age 11.07 ± 1.54 years; 23 males) were treated with monocular OK lenses (OK group), and 39 (mean age 10.64 ± 1.72 years; 22 males) with binocular HALs (HAL group). Changes in AL and spherical equivalent refraction (SER) from baseline at 3, 6 and 12 months were compared between eyes and groups. Kaplan-Meier estimation and Cox proportional hazard regression were performed to analyse the risk of myopia onset in the initially non-myopic eyes. Mean axial elongation in the myopic and non-myopic eyes at the 12-month follow-up visit were 0.17 ± 0.20 and 0.41 ± 0.26 mm in the OK group (p < 0.001) and 0.10 ± 0.15 and 0.12 ± 0.12 mm in the HAL group (p = 0.32), respectively. Compared with the OK group, the non-myopic eyes in the HAL group had less axial elongation, lower cumulative myopia incidence and percentage of participants with rapid myopic shift at the 6- and 12 month follow-up (all p < 0.05). Cox regression analysis showed that a higher initial SER decreased the risk of myopia onset significantly in the initially non-myopic eyes (B = -2.06; 95% CI, 0.03-0.49; p = 0.003). Monocular OK lenses suppressed axial elongation in the myopic eye and minimised anisometropia; however, the non-treated contralateral eye may experience faster myopia onset and myopic shift. Binocular HALs can effectively reduce axial elongation in both eyes of children with unilateral myopic anisometropia.