Introduction Meibomian gland dysfunction (MGD) is a common eye condition that causes excessive evaporation of tears by changing the tear film composition. Current treatments often fail to produce satisfactory results, which is mostly due to poor patient adherence. This study aimed to evaluate the effectiveness and safety of the MiBoFlo Thermoflo (R) on both subjective symptoms and objective signs in Chinese patients with MGD. Methods This prospective, randomized, controlled clinical trial included 108 eyes of 54 patients with MGD who were recruited in Beijing Tongren Hospital and randomized 1:1 to MiBoFlo (n = 54 eyes) or LipiFlow (R) (n = 54 eyes) treatment group. In the MiBoFlo group, patients received three 10-min treatments, each spaced 2 weeks apart, and the treatment was followed by eyelid compression each time. Patients in the LipiFlow group received a single 12-min treatment. The primary parameters measured included changes in Ocular Surface Disease Index (OSDI) score, Meibomian Glands Yielding Liquid Secretion (MGYLS) score, and Meibomian Glands Secretion (MGS) score from baseline to 2 months. The secondary parameters included tear meniscus height (TMH), non-invasive keratograph break-up time (NIKBUT), corneal fluorescein staining (CFS), and meibomian glands (MG) loss from baseline to 2 months. Safety parameters include visual acuity (VA), intraocular pressure (IOP), anterior segment, and facial skin. Results The OSDI, MGYLS, and MGS scores all improved from baseline to 1 month in both MiBoFlo and LipiFlow groups, and these improvements were maintained at 2 months. CFS score, NIKBUT, and MG loss showed no significant change in both groups. Conclusion As a portable and comfortable device, MiBoFlo can improve the treatment of MGD and achieve a sustained improvement in both symptoms and meibomian gland function lasting at least 2 months.