Reduction of the adverse effects of intraoperative intraocular pressure fluctuation referred to as post-occlusion surge on the intraocular structures is an important task for ensuring phacoemulsification safety. In this regard, the method to control infusion during phacoemulsification based on controlling the infusion and aspiration flow rates in combination with monitoring of vacuum parameters was developed. The study was aimed to provide comparative assessment of clinical and functional characteristics of the eye in patients after phacoemulsification using the new and already existing adaptive infusion control methods. A total of 38 patients aged 66.4 ± 7.8 years (15 males and 23 females) in the index group (Optimed Profi system with the use of new method) and 35 patients aged 68.7 ± 7.5 years (16 males and 19 females) in the control group (Centurion Vision System with Active Fluidics) underwent surgery due to cataract. The patients underwent comprehensive eye examination before surgery and on days 1, 7, 30, months 3, 6 after surgery. The smaller loss of corneal endothelial cells on months 3 and 6 after surgery was observed in patients of the index group with grade III and IV cataract (p < 0.05). Comparison of macular microcirculation parameters revealed the reduced FAZ area by month 6 of postoperative follow-up in the index group, along with the increased total vascular density of the deep vasculature (p < 0.001). A significant decrease in the total density of the superficial and deep vascular plexuses by month 6 of postoperative follow-up was observed in the control group (p < 0.05). The use of new adaptive infusion control method contributes to effective phacoemulsification of cataracts of varying density with the lower percentage of the corneal endothelial cells lost in the late postoperative period.