The invention discloses a biodegradable polymer composite with high thermal conductivity. The biodegradable polymer composite comprises heat-conducting nanofiller and a biodegradable polymer with a shape memory characteristic, wherein the heat-conducting nanofiller is arranged in the biodegradable polymer in order. The heat-conducting nanofiller without chemical modification is mixed with the biodegradable polymer, by use of the shape memory characteristic of the polymer, the heat-conducting nanofiller is arranged in order by stretch induced self-assembly, meanwhile, the heat-conducting nanofiller arranged in order is used as a physical crosslinking site to maintain the orientation state of the material, after the obtained material is heated secondarily, the filler still keeps high orientation, a constructed orientated structure facilitates lap joint of an ordered filler network with a small quantity of heat-conducting nanofiller, so that the production cost is reduced, the material density is reduced, the strength and ductility of the material are enhanced, and the thermal conductivity of the material is improved.