Objective To explore the application of modified Roux-en-Y gastrojejunostomy in gastric cancer surgery and its impact on gastrointestinal function. Methods A retrospective study was conducted on 152 gastric cancer patients admitted to the General Surgery Department of Xiangzhou District People's Hospital in Xiangyang City from January 2020 to January 2023. They were divided into two groups with 76 patients in each group based on different surgical methods. The control group was treated with open surgery and Billroth Ⅰ anastomosis, while the observation group was treated with open surgery and modified Roux-en-Y anastomosis. The serum tumor marker levels [carcinoembryonic antigen （CEA）, carbohydrate antigen 19-9 （CA19-9）, carbohydrate antigen 125 （CA125）, alpha-fetoprotein （AFP）] before and after surgery, postoperative gastrointestinal function indicators, and incidence of complications 6 months after surgery were compared between the two groups. Results After treatment, the serum levels of tumor markers CEA, CA19-9, CA125, and AFP in the two groups were lower than those before treatment （P<0.05）, but no differences were found between the two groups （P>0.05）. After treatment, the observation group had longer postoperative exhaust, bowel sound recovery, first meal intake, and first bowel movement time than the control group （P<0.05）. There was no statistically significant difference in the overall incidence rate of complications such as anastomotic leakage, infection, gastric bleeding, intestinal obstruction, gastric paralysis, physical deterioration, and poor surgical incision healing between the two groups of patients （P>0.05）. Conclusion The modified Roux-en-Y gastrojejunostomy for patients undergoing gastric cancer surgery does not increase the incidence of adverse reactions. However, it has a greater impact than Billroth Ⅰ anastomosis on the gastrointestinal tract of patients. In clinical practice, appropriate surgical methods should be selected based on the patient's condition to improve prognosis.