Purpose This retrospective study compared the long-term outcomes of single-incision laparoscopy-assisted Soave procedure (SILSP) with single-incision laparoscopy-assisted heart-shaped anastomosis (SILHSA) in patients with Hirschsprung disease (HSCR). Methods Patients diagnosed with HSCR that underwent SILSP or SILHSA between January 2009 and January 2015 at our institute were enrolled in this retrospective study. Data on the clinical characteristics, perioperative complications, and postoperative quality of life were retrospectively collected and analyzed. Results There were 109 patients in the SILSP group and 95 patients in the SILHSA group. No differences in clinical characteristics, including age, weight, hospitalization length, blood loss volume, and operation time, were noted between the two groups. The incidence rates of constipation and soiling were lower in the SILHSA group than those in the SILSP group. The SILHSA group showed lower scores in constipation and soiling compared with the SILSP group, indicating a better surgical outcome for patients receiving SILHSA procedure. Conclusion SILHSA is a feasible and reliable minimally invasive surgical procedure for patients with HSCR. Patients who underwent SILHSA had lower incidence rates of constipation and soiling than patients who underwent SILSP, suggesting that SILHSA could be a better choice for patients with HSCR.