PurposeTo compare changes in ocular aberrations in children wearing orthokeratology (ortho-k) lenses with a back optic zone diameter (BOZD) of 6 mm (6-MM group) or 5 mm (5-MM group) and their associations with axial elongation (AE) over two years.MethodsSeventy Chinese children, aged 6 to < 11 years, with myopia between − 4.00 to − 0.75 D, were randomly allocated to 5-MM and 6-MM groups. Ocular aberrations were measured, rescaled to a 4-mm pupil, and fitted with a 6th order Zernike expansion. Measurements, including axial length, were taken prior to commencing ortho-k treatment and then every six months over two years.ResultsAfter two years, the 5-MM group displayed a smaller horizontal treatment zone (TZ) diameter (by 1.14 ± 0.11 mm,P< 0.001) and less AE (by 0.22 ± 0.07 mm,P= 0.002) compared with the 6-MM group. A greater increase in total root mean square (RMS) of higher-order aberrations (HOAs), primary spherical aberration (SA) (\documentclass[12pt]{minimal}
				\usepackage{amsmath}
				\usepackage{wasysym} 
				\usepackage{amsfonts} 
				\usepackage{amssymb} 
				\usepackage{amsbsy}
				\usepackage{mathrsfs}
				\usepackage{upgreek}
				\setlength{\oddsidemargin}{-69pt}
				\begin{document}$${\mathrm{C}}_{4}^{0})$$\end{document}C40), and coma were also observed in the 5-MM group at all follow-up visits. The horizontal TZ diameter was significantly associated with changes in RMS HOAs, SA (RMS, primary and secondary SA), and RMS coma. After controlling for baseline parameters, RMS HOAs, RMS SA, RMS coma, and primary (\documentclass[12pt]{minimal}
				\usepackage{amsmath}
				\usepackage{wasysym} 
				\usepackage{amsfonts} 
				\usepackage{amssymb} 
				\usepackage{amsbsy}
				\usepackage{mathrsfs}
				\usepackage{upgreek}
				\setlength{\oddsidemargin}{-69pt}
				\begin{document}$${\mathrm{C}}_{4}^{0})$$\end{document}C40)and secondary (\documentclass[12pt]{minimal}
				\usepackage{amsmath}
				\usepackage{wasysym} 
				\usepackage{amsfonts} 
				\usepackage{amssymb} 
				\usepackage{amsbsy}
				\usepackage{mathrsfs}
				\usepackage{upgreek}
				\setlength{\oddsidemargin}{-69pt}
				\begin{document}$${\mathrm{C}}_{6}^{0})$$\end{document}C60)SA were significantly associated with AE.ConclusionsOrtho-k lenses with a smaller BOZD created a smaller horizontal TZ diameter and a significant increase in total HOAs, total SA, total coma, and primary SA and a decrease in secondary SA. Of these ocular aberrations, total HOAs, total SA, and primary SA were negatively correlated with AE over two years.Trial registration: ClinicalTrial.gov, NCT03191942. Registered 19 June 2017,https://clinicaltrials.gov/ct2/show/NCT03191942.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40662-023-00344-3.