Percutaneous endoscopic transforaminal discectomy (PELD) is a new minimally invasive spine surgery for patients with lumbar disc herniation (LDH). Based on the 3-year follow-up data, the effect of PELD on the clinical outcomes of patients with LDH through a retrospective cohort study was analyzed in this article, so as to provide guidance for clinical selection of surgical options. The clinical data of 150 patients with LDH admitted to our hospital from January 2019 to October 2020 were retrospectively analyzed. According to the surgical methods recorded in the medical record system, the patients were divided into the open lumbar microdiscectomy (OLM) group (n = 50) and the PELD group (n = 100). The surgical and postoperative recovery indicators of the two groups were compared after matching. These included incision length, intraoperative blood loss, operation time, postoperative ambulation time and hospital stays, recovery rate, short-term complication rate, Lumbar visual analogue scale (VAS) score, and Oswestry Disability Index (ODI) score. Compared with the OLM group, the PELD group had shorter incision length, shorter operation time, shorter postoperative ambulation time, shorter hospital stays, less intraoperative blood loss, lower short-term complication rate, lower lumbar pain and dysfunction scores at 3 months, 6 months, and 1 year after operation, higher short-term excellent-and-good recovery rate, and higher quality-of-life scores at 3 years after operation (p < 0.05). Compared with OLM, PELD in the treatment of LDH patients can reduce the operation time, blood loss, and length of hospital stays, suggesting a short-term postoperative recovery effect. Compared with OLM, PELD can also reduce the incidence of short-term complications, enhance the effect of pain control and improvement of dysfunction in the medium term, and improve the long-term quality of life.