Objective To investigate the clinical effects of prophylactic transverse colostomy on gastrointestinal function recovery and complications in patients undergoing completely laparoscopic transabdominal approach partial intersphincteric resection (CLAPISR) of low rectal cancer. Methods We retrospectively analyzed the data of 74 patients with low rectal cancer who were treated with prophylactic transverse colostomy (Group A, n = 34) or without prophylactic transverse colostomy (Group B, n = 40). Surgery-related indicators, nutritional status indicators, systemic stress response indicators, and complications were compared between the two groups. Results On postoperative day 5, the C-reactive protein concentration and white blood cell count were not significantly different between the two groups; however, the serum concentrations of total protein and albumin were higher in Group A than in Group B. Within 26 months postoperatively, the total incidence rate of complications was not significantly different, but the incidence rate of anastomotic leakage was lower in Group A than in Group B. Conclusion Prophylactic transverse colostomy based on CLAPISR can lead to faster recovery of gastrointestinal function, better improvement of postoperative nutritional indicators, and a lower incidence of anastomotic leakage. These characteristics are conducive to the rapid recovery of patients, making this procedure worthy of clinical application.