Purpose: To compare the short-term changes in cornea, retina and choroid of femtosecond laser-assisted cataract surgery (FLACS) with conventional phacoemulsification (CPS) in high myopia patients with cataract. Setting: Affiliated Hospital of Nantong University, Jiangsu Province, China. Design: Prospective single-center study. Method: Demographics, ocular clinical features, ultrasound power, absolute phacoemulsification time, and effective phacoemulsification time were recorded for each patient. Endothelial cell density (ECD), central corneal thickness (CCT), best corrected distance visual acuity (CDVA), intraocular pressure(IOP), center foveal thickness(CFT), subfoveal choroidal thickness (SFCT) and choroidal vascularity index (CVI) were evaluated preoperatively and at 1 week, 1 month, and 3months postoperatively. Intraoperative parameters and intraoperative /postoperative complications were recorded. Results: Ninety-seven eyes (46 eyes and 51 eyes in the FLACS and CPS groups, respectively) were included and analyzed. Cumulative dissipated energy was lower in FLACS group compared with CPS group (P <0.05). The increase in CCT was significantly lower in the FLACS group compared with the CPS group at 1week and 1month (P <0.05). CDVA and IOP were similar in both groups at the final visit ( P > 0.05). The ECD decreased was lower among CPS patients compare with FLACS patients. CFT, SFCT and CVI increase in both groups but were increase more in CPS group with high myopia patients. No serious complications occurred in either group. Conclusions: FLACS is a more safety and effective in cataract patients with high myopia. It has advantages in effectively reducing EPT and promoting faster recovery of the cornea, macular and choroidal thickness.