Purpose: To explore the effect of electrode structure on welding quality by modifying the structure of magnesium alloy electrode. Methods: Two novel electrodes were designed in this study, including one with a circle (C) surface and the other with a square and arched (SA) surface. The designed electrodes were compared to a control electrode with a smooth surface in terms of temperature distribution, thermal damage to tissue, and effective welding area. Finite element analysis was used to analyze the stress and strain of all electrodes and thermal damage to the tissue. Results: Pressure applied to the designed electrodes was within the elastic limit, and the deformation was less than 1%. The highest temperature of SA electrode (99.6 ℃) was similar to that of the control (100 ℃), while that of C electrode (106 ℃) was higher than the control. The mean temperature at the welding site in intestine of the control electrode was significantly higher than that of the other two electrodes. Besides, the mean temperature of C electrode was also slightly higher than that of SA electrode. The tissues welded by the control electrode, C electrode and SA electrode were completely necrotic within an axial distance of 2.546 mm, 2.079 mm, and 1.835 mm from the edge of the welding area, respectively. Conclusion: SA electrode has the lowest thermal damage compared with the other two electrodes due to smaller effective welding area. Therefore, SA electrode is better than the other two electrodes.