Purpose To quantitatively evaluate the lipid layer thickness (LLT) and blinking in children with or without allergic conjunctivitis (AC), and to compare those between the different types of AC. Methods For this case-control study, 81 children with symptomatic AC with an average age of 9.62 ± 2.67 years were enrolled and subdivided according to the subtypes of AC, including seasonal/perennial allergic conjunctivitis group and vernal keratoconjunctivitis (VKC)/atopic keratoconjunctivitis (AKC) group. Another 82 age-matched healthy children were enrolled as control group. All subjects underwent routine eye examination and measurements of LLT, the number of incomplete or total blinking, partial blinking rate by the LipiView interferometer over a 10-s period. Other ocular surface assessment included fluorescein tear breakup time (TBUT), lower tear meniscus height, meibomian gland loss (MGL), meibum expressibility and quality. Results Pediatric patients with AC had significant thinner LLT, shorter TBUT, decreased total blinking but increased partial blinking rate, especially in those with VKC/AKC (all P < 0.05). A significant deterioration of meibomian gland parameters was observed in AC group when compared with control subjects, demonstrated by severe upper and lower MGL, lid margin abnormalities, decreased meibum expressibility, and abnormal meibum quality, all of which were worse in the severe type of AC (all P < 0.05). Thinner LLT was significantly correlated with decreased TBUT (β = 3.666, P < 0.001) and severity of upper MGL (β = − 7.701, P = 0.002). Conclusion Decreased LLT and blinking disorders in pediatric patients with AC may contribute to lipid layer deficiency in the long run, which should be considered and appropriately diagnosed for a more precise treatment.