Objective To analyze the influence of phacoemulsification on the morphological changes of corneal endothelial cells （CEC）. Methods This was a self-controlled study. Fifty patients （50 eyes） under phacoemulsification and intraocular lens implantation were analyzed. The cornea was divided into five quadrants including central， superior， inferior， nasal and temporal. The corneal specular microscope （CSM） was used to collect CECs’ images and data from five sections （central， superior， inferior， nasal and temporal） in each quadrant （25 sections in total）. The images were collaged， and the data were measured by Image J 1.38X. All the conventional CSM parameters and new parameters including proportion of cell types， variations of cell side length and cell angle were analyzed respectively. The difference between parameters in the central and the other quadrants were compared. Results All the surgeries on 50 eyes were carried out successfully， and there was no complications during and post operation except for slight corneal edema limited to the incision area. Comparing the data before and 12 months after the operations in 25 sections， there were significant difference （both P<0.01） in the cell density （CD） （changed from 2 854±290 mm2 to 2 035±150 mm2， t=17.86） and the average cell area （Save） （changed from 351±29 μm2 to 606±59 μm2， t=27.14）. There was no significant difference in HEX% （pre-operation was 63.5±4.2 and 12 months post-operation was 61.2±3.7）， the variation of side length of CECs （pre-op was 19.7±2.5 and post-op was 20.2±2.2）， the variation of angle of CECs （pre-op was 158.4°±27.5° and post-op was 155.3°±19.1°）， the portion of polygon cells （pre-op was 12.3%±2.7%， post-op was 11.2%±3.4%）， and the portion of pentagon cells （pre-op was 4.8%±2.2% and post-op was 5.7%±2.4%）. There were significant difference in the number of CEC dark zone （pre-op was 0.31±0.14 and post-op was 0.83±0.25）， and the area of CEC dark zone （pre-op was 81.3±55.2 and post-op was 244.9±131.6） （t=18.65 and t=5.25， both P<0.01）. Twelve months after surgery， compared all the parameters above in central quadrant to those in other quadrants， there were significant difference （all P<0.01）. Conclusion CEC were not equally-distributed 12 mon after phacoemulsification， collecting the CEC data from multiple quadrants and multiple sections after phacoemulsification is a better way to show the characteristics of CEC.