Objective: To compare the efficacies of a single thermodynamic treatment system (LipiFlow®) and warm compresses used for 3 months in patients with a moderate severity of meibomian gland dysfunction (MGD). Methods: This prospective, randomized, controlled clinical study enrolled 28 patients (22 females, 6 males; mean age, 53.9 ± 14.8 years) diagnosed as having moderate MGD by plugging at the meibomian gland orifices between one-third and two-thirds of lid margins and at least one of the following: a Standard Patient Evaluation of Eye Dryness (SPEED) questionnaire score of 6-12; a lipid layer thickness (LLT) score of 40-70 Interferometric Color Units; upper eyelid meiboscore of 1-2; and 3-6 expressible meibomian glands (EMGs) in the lower eyelid. Both eyes of each patient were randomized into study and control eyes. Study eyes were treated with a single, 12-minute LipiFlow® system, while control eyes received 5-minute warm compresses twice daily for 3 months. The dry eye symptoms, the number of EMGs, and LLTs were evaluated. Results: There were no significant differences in the dry eye symptoms, number of EMGs, and LLTs for both groups at baseline and at each follow-up. However, the total SPEED scores for the LipiFlow® group reduced significantly from baseline at each follow-up until 6 months. As to the warm compress group, the total SPEED scores reduced significantly from baseline at each follow-up until 3 months. Conclusion: The single LipiFlow® treatment and twice-daily warm compresses relieved the dry eye symptoms of patients with a moderate severity of MGD compared with their baseline symptoms, despite no statistical differences in the dry eye symptoms, number of EMGs, and LLTs of both treatments.