In vivo laser scanning confocal microscopy (LSCM) has been widely used to evaluate the alterations caused by ocular surface diseases at a cellular level in the living eye. In this review, we focus on its use in the diagnosis of pterygium, meibomian gland (MG) disease, and chemical burns. Histopathologic changes occurring in pterygium can be examined in situ using in vivo LSCM. Alterations at the junction of the pterygium and the cornea, which cannot be observed in excised tissue samples, can be observed. MGs play an important role in maintaining the health of the ocular surface. Meibomian gland dysfunction (MGD) is one of the most common ocular surface diseases. The use of in vivo LSCM helps in the diagnosis of MGD and provides a way to examine the microstructure of MG acinar units and measure their size. In vivo LSCM also provides a new perspective in understanding the contribution of the MG to the health of the ocular surface. Chemical burns are one of the most common ocular injuries, and in vivo LSCM can provide images of the goblet cells on the corneal surface. This is a hallmark of limbal stem cell deficiency. The application of in vivo LSCM to assessing chemical burns requires extension, allowing for evaluation of the limbus structure and ocular surface changes after reconstructive ocular surgery.