To examine the influence of subfoveal choroidal thickness (SFCT) and choroidal vascularity index (CVI) on axial length (AL) elongation over a 2-year period in highly myopic children. In this is prospective, longitudinal, observational study, 163 participants (74%), who were 8 to 18years of age with bilateral high myopia (sphere ≤ -6.0 D) and without pathologic myopia, completed follow-up visits over 2years. All participants underwent baseline and follow-up ocular examinations, including swept-source optical coherence tomography (SS-OCT) and AL measurements. SFCT and CVI were derived from SS-OCT scans using a deep-learning-based program for choroidal structure assessment. The mean age of the participants at baseline was 15.0years (±2.3), with males constituting 47% of the cohort. An inverse relationship was observed between AL elongation and increases in baseline age, baseline SFCT, and CVI, as well as a decrease in baseline AL. Adjusting for other factors, every 10-µm increase in SFCT and each 1% increase in CVI were associated with decreases in AL elongation of 0.007mm (95% confidence interval [CI], -0.013 to -0.002; P = 0.011) and 0.010mm (95% CI, -0.019 to 0.000; P = 0.050), respectively. The incorporation of SFCT or CVI into predictive models improved discrimination over models using only age, gender, and baseline AL (both P < 0.05, likelihood ratio test). Our findings suggest a possible association between a thinner choroid and increased AL elongation over 2 years in children with high myopia, after adjusting for potential baseline risk factors such as age, gender, and initial AL.