High damping magnesium alloys have poor mechanical properties, so it is necessary to investigate the damping properties of high-strength wrought magnesium alloys to effectively reduce vibration and noise in mechanical engineering. The aim of this work is to improve the mechanical damping performance of a novel high-strength Mg-13Gd-4Y-2Zn-0.5Zr magnesium alloy by optimising the heat treatment process. The mechanical damping coefficient, considering not only damping capacity but also the yield strength, is selected as one of the evaluation indexes. The other evaluation index is the tensile strength. The solid solution and ageing treatment were optimised by Box-Behnken method, an efficient experimental design technique. Heat treatment experiments based on the optimal parameters verified that the best process is a solution at 520 °C for 10 h followed by ageing at 239 °C for 22 h. The damping coefficient reaches 0.296, which is 73.1% higher than that before heat treatment. There was a good agreement between the experimental and Box-Behnken predicted results. The microstructure, morphology and composition of the second phases after heat treatment were analysed by SEM, XRD and EDS. Due to the high content of alloying elements in Mg-13Gd-4Y-2Zn-0.5Zr alloy, there are a large number of second phases after heat treated. They mainly include layer, short rod-shaped, bulk long period stacking order (LPSO) Mg12YZn and granular Mg5Gd phases. It was found that the area fraction of the second phases has an extreme effect on the damping capacity and short rod-shaped LPSO can effectively improve the damping capacity of heat-treated Mg-13Gd-4Y-2Zn-0.5Zr alloy. The volume fraction of the second phases was analysed by ImageJ software. It was concluded that the smaller the area occupied by the second phases, the better the mobility of the dislocation, and the better the damping performance of the alloy. The statistical analysis results obtained using ImageJ software are consistent with the experimental results damping capacity.