Purpose To explore the effect of Meibomian Thermal Pulsation LipiFlow (R) on obstructive and hyposecretory meibomian gland dysfunction. Methods Twenty-five subjects diagnosed with obstructive meibomian gland dysfunction (OMGD) and another 25 hyposecretory meibomian gland dysfunction (HMGD) patients were collected receiving the unilateral treatment with LipiFlow (R). We evaluated the parameters variables including Standard Patient Evaluation of Eye Dryness (SPEED), Ocular Surface Disease Index (OSDI), Schirmer I test (SIT), noninvasive keratographic breakup time (NIKBUT), tear meniscus height (TMH), and lipid layer thickness (LLT), partial blink rate (PBR), meibomian gland loss, meibomian gland morphology with LipiView (R). Meibomian gland expressibility and secretion quality were evaluated for OMGD subjects. All the results were recorded pre-therapy and 4 weeks, 8 weeks, 12 weeks post-therapy. Results SPEED, OSDI, and PB decreased, meanwhile, NIKBUT, TMH, SIT, and LLT increased compared with baseline in both groups after treatment (P < 0.001), whereas the magnitude of the improvement in the OMGD group was greater than that in the HMGD group (P < 0.001). There was no significant posttreatment structural meibomian gland change in both groups. The meibomian gland expressibility and secretion quality score increased after treatment in the OMGD group (P < 0.001). Conclusions The Meibomian Thermal Pulsation LipiFlow (R) is effective for both obstructive and hyposecretory meibomian gland dysfunction and the therapeutic effect on obstructive meibomian gland dysfunction is greater than that on hyposecretory meibomian gland dysfunction.