Objective To investigate the effect of 3S jejunal interposition anastomosis in digestive tract reconstruction after radical resection for early gastroesophageal junction adenocarcinoma. Methods One hundred and eighteen patients of early gastroesophageal junction adenocarcinoma who were planned to receive radical proximal gastrectomy from February 2011 to August 2015 were prospectively enrolled and randomly divided into two groups by table of random number, including observation group (3S jejunal interposition) and control group (esophageal remnant gastric posterior wall anastomosis), with 59 patients in each group. Postoperative complications, operative time, nutritional parameters and postoperative quality of life were compared between two groups. Results The operation time in observation group was (152.3 ± 13.1) min, in control group was (146.0 ± 12.5) min, and there was no significant difference (P>0.05). The rate of complication in observation group was 8.5%(5/59), in control group was 13.6%(8/59), and there was no significant difference (P>0.05). The levels of total protein, albumin, hemoglobin, and Vitamin B126, 12, and 18 months after operation in observation group were significantly higher than those in control group (P<0.05). The rate of reflux esophagitis 6, 12 and 18 months after operation in observation group was significantly lower than that in control group (P<0.05). The gastric emptying time 6, 12 and 18 months after operation in observation group was significantly prolonged, compared with that in control group (P<0.05). The scores of whole quality of life, emotional function, body function, pain, tired, appetite, nausea and vomiting, diarrhea and constipation 6 and 18 months after operation in observation group were significantly better than those in control group (P<0.05). Conclusions The 3S jejunal interposition anastomosis in digestive tract reconstruction after radical resection for early gastroesophageal junction adenocarcinoma is a better method. The effect of antirelux is better and can improve the nutriture and quality of live for long time.