In this study, we aim to evaluate the risk factors of myopia undercorrection in recipients of second-generation keratorefractive lenticule extraction (KLEx) surgery. A retrospective case-control study was performed, and patients who received second-generation KLEx surgery were enrolled. The cases with myopia undercorrection were matched to non-myopia undercorrection cases with a 1:4 ratio according to age, and a total of 22 and 88 eyes were categorized into the undercorrection and control groups, respectively. Demographic, refractive, topographic, and surgical data were collected preoperatively. A generalized linear model was operated to evaluate the potential risk factors for myopia undercorrection. The uncorrected distance visual acuity (UDVA) at three months postoperation was significantly better in the control group ( = 0.006), and residual myopia and SE were significantly higher in the undercorrection group during the whole follow-up period (all < 0.001). The UDVA value showed a trend of improvement in the control group ( < 0.001), and the changes to SE and residual myopia were significantly lower in the control group (both < 0.001). Regarding the risk factors for myopia undercorrection in the whole population and the high-myopia population, a higher manifest sphere power, higher steep keratometry (K), higher topographic cylinder, lower central corneal thickness (CCT) at apex, higher CCT difference and lower residual stromal thickness (RST) correlated to myopia undercorrection (all < 0.05). In the low-myopia population, only higher myopia and lower RST correlated to myopia undercorrection (both < 0.05). In conclusion, a high-sphere power and irregular topographic pattern correlated to myopia undercorrection after the second KLEx surgery, especially for individuals with high myopia.