AIM: To investigate the factors influencing meibomian gland atrophy (MGA) in children with allergic conjunctivitis (AC). METHODS: In this cross-sectional study, 60 children with AC aged 6-17y and 20 age-matched children without signs or symptoms of ocular surface dysfunction were included. Information on the duration of AC, untreated time, electronic screen time (EST), outdoor exercise time, body mass index (BMI), and frequency of eye rubbing was collected using a health history form. The Standard Patient Evaluation of Eye Dryness (SPEED) score was used for dry eye assessment. Images of the meibomian glands (MGs) were obtained using Keratograph 5M, and the rate of meibomian gland atrophy (MGAR) was calculated using Image J. All subjects underwent routine eye examinations. RESULTS: The average age of the AC group was 10.43±2.75y (range 6-17y) and 10.35±3.42y (range 6-14y) in the control group. The MGAR in the AC group was 33.42%±11.91%, significantly higher than that in the control group (18.10%±11.74%, P<0.001). Moreover, the MGAR in younger children (aged 12 and below) was significantly higher than in older children (P<0.05). Multi-factor linear regression analysis revealed that EST non-projector was a risk factor for MGAR (β=0.332, 95%CI 0.04-0.22, P=0.004), while outdoor exercise time was a protective factor against MGAR (β=-0.407, 95%CI -0.39 to -0.10, P=0.001). The untreated time of AC was identified as a risk factor for MGAR (β=0.24, 95%CI 0.07-1.98, P=0.037), and the frequency of eye rubbing was associated with MG distortion score (P=0.00). CONCLUSION: Children with AC exhibit exacerbate MGA, with the degree of atrophy worsening as the untreated time of AC prolongs. Children under 12 years old show a higher MGAR, and EST non-projector negatively impacts MGA, while increased outdoor exercise time acts as a protective factor against MGA.