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.