Purpose <p>We compared the efficacy of intense pulsed light (IPL) therapy alone and combined with eyelid margin cleaning using a deep cleaning device for the treatment of meibomian gland dysfunction (MGD).</p> Methods <p>In this single-center, investigator-masked randomized controlled trial, eyelid margin cleaning was performed using an OCUFACE device (Guangzhou Ocuface Biotechnology Co., Ltd.). Treatment efficacy was compared between the intervention and control groups based on changes in the clinical indicators from baseline. The primary outcomes were the improvement of meibomian gland secretion quality, changes in the Ocular Surface Disease Index (OSDI) score, and the improvement of tear film stability (e.g., tear break-up time).</p> Results <p>Data from 120 eyes of 60 patients with MGD were included in the final analysis. The changes in the OSDI (<i>p</i> = 0.021) and nasal-region meibomian gland function (<i>p</i> = 0.022) differed significantly between groups. The change in temporal-region meibomian gland function had a similar trend, but the difference was not significant (<i>p</i> = 0.25). The mean value for lower-eyelid meibomian gland loss was significantly lower in the intervention group than in the control group (0.85 vs. 1.12, <i>p</i> = 0.045). The median NIBUT after treatment was significantly longer in the intervention group than in the control group (5.45 vs. 3.05&#xa0;s, <i>p</i> = 0.008).</p> Conclusion <p>IPL therapy combined with deep eyelid margin cleaning alleviates meibomian gland orifice obstruction and improves tear film stability. This study establishes a new treatment paradigm, with a shift from passive thermal modulation to active ductal remodeling.</p> Trial registration <p>This research was retrospectively registered in the Chinese Clinical Trial Registry (CTR2400092860, 2024/11/25).</p>