OBJECTIVES: This study aimed to compare the efficacy of local excision (LE) and intersphincteric resection (ISR) in patients with locally advanced rectal cancer who achieved a significant or complete pathological response following neoadjuvant chemoradiotherapy. METHODS: We performed a retrospective analysis of data from patients with stage ypT0-1ycN0 low rectal cancer after neoadjuvant chemoradiotherapy who underwent LE or ISR between June 2016 and June 2021. Baseline characteristics, short-term outcomes, long-term oncological outcomes, and functional outcomes, were compared between the two groups. To reduce the selection bias, inverse probability of treatment weighting (IPTW) was performed. RESULTS: This study included 106 patients (LE group: n = 51, ISR group: n = 55). There were significant differences in baseline characteristics between the two groups (P < 0.05). After IPTW, there were almost no significant differences in baseline data between the two groups. The LE group showed less postoperative complications and better function outcomes compared to the ISR group. The LE group had significantly lower rates of complications (13.7% vs. 36.4%, P = 0.014). There were no significant differences between the two groups in terms of long-term oncological outcomes. CONCLUSIONS: For patients with locally advanced low rectal cancer achieving significant or complete pathological response after neoadjuvant therapy, both LE and ISR present comparable oncological outcomes. Yet, LE seems to show more advantages in terms of postoperative complications and functional outcomes. These findings offer important insights for surgical decision-making, emphasizing the necessity to consider both oncological and functional outcomes in selecting the optimal surgical approach.