The invention relates to the technical field of intelligent materials, and provides a shape memory composite material based on polyhydroxyalkanoate. The composite material comprises the following components in parts by weight: 30-70 parts of polyhydroxyalkanoate, 30-70 parts of polyurethane, and 0-10 parts of compatilizer, wherein the molecular weight of polyhydroxyalkanoate is greater than 10,000 g / mol; polyurethane is prepared by isocyanate and micromolecular alcohol or amine with the molecular weight less than 600 g / mol; and the content of isocyanate and micromolecular alcohol or amine in polyurethane is greater than 70 wt%. The invention further provides a preparation method of the material based on polyhydroxyalkanoate, and the application of the material based on polyhydroxyalkanoate in the aspects of biomedical engineering, textile, toys and daily supplies. The material has good biological compatibility, does not form thrombi when contacted with blood, is integrated with tissue cells well, and has a shape memory function, the shape fixing rate is greater than 80%, and the shape recovery rate is greater than 80%.