Abstract There is a great clinical need for biodegradable materials, which were used as pins of circular staplers, for gastrointestinal reconstruction in medicine. In this work we compared the effects of the Mg–6Zn and the titanium alloys on collagen metabolism in the healing of the intestinal tract in vivo. The study included Sprague-Dawley rats and their effect was compared on rat’s intestinal tract, using serum magnesium, radiology, and immunohistochemistry in vivo. Radiographic and scanning electron microscope evaluation confirmed the degradation by Mg–6Zn alloy during the implantation period. Biochemical measurements including serum magnesium, creatinine, blood urea nitrogen and glutamic–pyruvic–transaminase proved that degradation of Mg–6Zn alloy showed no impact on serum magnesium and the function of other important organs. Superior to titanium alloy, Mg–6Zn alloy enhanced the expression of collagen I/III and relatively suppressed the expression of MMP-1/-13 in the healing tissues, leading to more mature collagen formation at the site of anastomosis. In conclusion, Mg–6Zn alloy performed better than titanium alloy on collagen metabolism and promoted the healing of intestinal anastomosis. Hence, Mg-6Zn may be a promising candidate for use of stapler pins for intestinal reconstruction in the clinically.