Background Percutaneous endoscopic lumbar discectomy (PELD) is a relatively safe and effective minimally invasive surgery in the treatment of calcified lumbar disc herniation (CLDH). However, studies on percutaneous endoscopic interlaminar discectomy (PEID) and percutaneous endoscopic transforaminal discectomy (PETD) for CLDH have rarely been reported. This research aimed to compare the clinical efficacy of PEID and PETD for L5-S1 CLDH. Methods We retrospectively analyzed 54 consecutive patients with L5-S1 CLDH treated with PELD at our institution from August 2016 to August 2020. Patients were divided into PEID group (n = 28) and PETD (n = 26) group according to the surgical methods. The demographic characteristics and surgical results of the two groups were compared. Clinical outcomes were estimated by the visual analog scale (VAS) for leg pain, Oswestry disability index (ODI) and modified MacNab criteria. Results All patients were successfully operated on by PEID or PETD. No significant differences in the demographic characteristics, intraoperative blood loss, postoperative hospital stay and complication rate were noted between the PEID and PETD groups. The excellent and good rates in the PEID group were similar to those in the PETD group (89.29% vs 88.46%, P = 1.000), whereas the PEID group exhibited superior results for operative time (min) (64.61 +/- 5.60 vs 85.58 +/- 8.52, P < 0.001) and fluoroscopy times (n) (2.93 +/- 0.90 vs 13.35 +/- 2.30, P < 0.001) compared with the PETD group. Conclusions PEID has achieved good clinical efficacy as PETD for L5-S1 CLDH. Compared with PETD, PEID has the advantages of shorter operative time and a reduced number of fluoroscopy times in the treatment of CLDH.