Background To observe the effects of chalazion and its treatments on meibomian gland function and morphology in the chalazion area.Methods This nonrandomized, prospective observational clinical study included 58 patients (67 eyelids) who were cured of chalazion, including 23 patients (23 eyelids) treated with a conservative method and 35 patients (44 eyelids) treated with surgery. Infrared meibomian gland photography combined with image analysis by ImageJ software was used to measure the chalazion area proportion. Slit-lamp microscopy was employed to evaluate meibomian gland function, and a confocal microscope was used to observe meibomian gland acinar morphology before treatment and 1 month after complete chalazion resolution.Results At 1 month after chalazion resolution, the original chalazion area showed meibomian gland loss according to infrared meibomian gland photography in both groups. In patients who received conservative treatment, the meibomian gland function parameters before treatment were 0.74±0.75, 0.48±0.67, and 1.22±0.60, respectively. One month after chalazion resolution, the parameters were 0.35±0.49, 0.17±0.49, and 0.91±0.60, respectively; there was significant difference (P<0.05). The proportion of the chalazion area before treatment was 14.90 (11.03, 25.3), and the proportion of meibomian gland loss at 1 month after chalazion resolution was 14.64 (10.33, 25.77); there was no significant difference (P>0.05). In patients who underwent surgery, the meibomian gland function parameters before surgery were 0.93±0.87, 1.07±0.70, and 1.59±0.76, respectively, and at 1 month after chalazion resolution, they were 0.93±0.82, 0.95±0.75, and 1.52±0.70, respectively; there was no significant difference (P>0.05). The proportion of the chalazion area before surgery was 14.90 (12.04, 21.6), and the proportion of meibomian gland loss at 1 month after chalazion resolution was 14.84 (11.31, 21.81); there was no significant difference (P>0.05). The acinar structure could not be observed clearly in the meibomian gland loss area in most patients.Conclusions Chalazion causes meibomian gland loss, and the range of meibomian gland loss is not related to the treatment method but to the range of chalazion itself. A hot compress as part of conservative treatment can improve meibomian gland function at the site of chalazion in the short term.