AIM: The most recent and innovative AquaLase liquefaction technology has offered an alternative to lens extraction. Many studies have investigated its functions and advantages. This article focuses on evaluating the in vivo microscopic cornea changes after AquaLase liquefaction by using a laser confocal microscope. METHODS: In this perspective, randomized case study, 37 eyes of 35 patients submitted to cataract surgery were chosen to undergo AquaLase liquefaction cataract extraction. Each patient was assessed before the operation, on the 1st, 7th, and 30th postoperative days, and 6 months after the cataract extraction. The morphologies and quantitative comparisons of corneal cells and corneal nerves layer by layer were evaluated in vivo with the Heidelberg Retina Tomograph III-Rostock Cornea Module (HRT-III RCM) confocal microscope. ANOVA and Post-Hoc Bonferroni test were carried out to compare the results pre- and post-operation. RESULTS: ANOVA results indicated no post-operation changes for epithelium and anterior stroma cells. Irregular segments of sub-basal nerve fiber were most pronounced seven days post-operation. In the mid and posterior stroma, keratocytes were obvious compared with the preoperative condition. Corneal endothelium cells became obviously swollen in cytoplasm and nucleus. The mid and posterior stroma cell density decreased from the 1st to 7th postoperative days (P<0.05). The corneal endothelium cell density decreased (P<0.05) and did not revert to the preoperative level after six months (P<0.05). CONCLUSION: Slight microstructural abnormalities were identified in the corneal recovery process after AquaLase liquefaction. AquaLase liquefaction cataract extraction is safe for cornea.