Background: Magnetic compression for creating gastrojejunostomy has many advantages according to previous studies. However, following mechanical device release after healing, the anastomotic stenosis becomes the pivotal point. Methods: Rectangle-shaped magnets were used for magnetic compression in rabbits. Both paclitaxel-loaded magnets and a strategy of pyloric ligation were chosen to improve the gastrojejunostomy. Based on these choices, the half-capsule was applied to occlude the pylorus after anastomotic formation. The size and patency of the anastomoses were analyzed to evaluate the efficacy of these approaches. A histological examination was also performed. Results: The positive effect of ligating the pylorus on gastrojejunostomy was significantly greater than that achieved using paclitaxel-loaded magnets during either short- or long-term follow-up. There were fewer scar tissue and collagen fibers at the anastomotic site in the treatment group than in the control group. The anastomotic aperture was of great interest at 9 months after the ligation of the pylorus following magnetic compression. In the view of the jejunum, although the aperture was barely visible, gastric juice was continuously spilling through it like a spring, and the aperture was clearly visible from the stomach side. All half-capsules failed to block the pylorus. Conclusion: The effect of paclitaxel on maintaining gastrojejunostomy patency was temporary. The ligation of the pylorus ensured the long-term patency of gastrojejunostomy, and the aperture was comparable to the pylorus which could play an anti-reflux role. Further studies for the sort of gastrointestinal aperture are being planned