Background: To analyze the morphological changes of meibomian glands in patients with recurrent and primary meibomian gland cyst under in vivo confocal microscope (IVCM). Methods: A cross-sectional study was performed in Shantou International Eye Center from September 2018 to April 2019. Ten patients with recurrent meibomian cyst, 10 patients with primary meibomian cyst and 10 control subjects were selected in this clinical trial. All subjects received routine ophthalmologic examination and IVCM examination. IVCM examination parameters included open area of meibomian gland, and the maximum and minimum diameter of meibomian gland opening. Relevant parameters were analyzed and statistically compared among different groups. Results: The average minimum diameter of meibomian glands opening in the recurrent meibomian gland cyst group was (109.08±49.96) μm, the average maximum diameter of meibomian glands opening was (144.95±68.10) μm, and the median open area of meibomian gland was 11 621.62 (3 976.49–24 828.82) μm2 . In the primary meibomian gland cyst group, the average minimum diameter of meibomian glands opening was (101.53±29.55) μm, the average maximum diameter of meibomian glands opening was (130.08±45.21) μm, and the median open area of meibomian gland was 10 615.07 (5 813.29–18 275.44) μm2 . The opening of meibomian glands in both the recurrent and primary meibomian gland cyst groups was enlarged, which significantly differed from that in the control group (both P<0.05). No statistical significance was noted between the recurrent and primary meibomian gland cyst groups (P>0.05). The acinus structure around the gland tube was manifested with serious hypertrophic scar complicated with inflammatory cell infiltration. Conclusion: IVCM can detect the morphological changes of meibomian glands in meibomian gland cyst patients. The IVCM findings of recurrent and primary meibomian gland cyst are different.