The aim of this study is to compare the postoperative quality of life (QoL) and survival outcomes in lower rectal cancer (LRC) patients who undergo either laparoscopic- intersphincteric resection or extralevator abdominoperineal excision (L-ELAPE) after long-course neoadjuvant chemoradiation therapy (nCRT). This prospective, single-center, non-randomized, controlled, non-blinded, phase I/II clinical trial is designed to enroll 159 eligible LRC patients who achieved favorable response to long-course nCRT (2 × 25 Gy). After informed consent, the patients will be assigned into the laparoscopic intersphincteric resection group or L-ELAPE group according to their own will. Standard radical laparoscopic surgeries will be performed for every participant. Then every participant will be followed up for 3 years. The primary outcomes are scores of QoL questionnaire-core 30, QoL questionnaire-colorectum 29, Wexner incontinence score, International Prostate Symptom Score (for male), International Index of Erectile Function-5 (for male) and Female Sexual Function Index (for female). The secondary outcomes consist of incomplete circumferential resection margin rate, 3-year local recurrence, 3-year disease-free survival, 3-year overall survival and other surgical outcomes. This is the first prospective clinical controlled trial to assess postoperative QoL and efficacy for LRC patients after favorable long-course nCRT. The result is expected to provide new evidence for a more detailed individualized treatment guideline for LRC. This trial was registered at Chinese Clinical Trial Registry (ChiCTR1800017512; ChiCTR.org) on August 2, 2018.