Objective To investigate a method for preparing decellularized rat heart scaffold, and to detect and evaluate the decellularized scaffold. Methods The decellularized rat heart scaffold was prepared by retrograde perfusion with a combination of enzymatic and Triton X-100 detergent methods to remove the populations of resident cells, and then the decellularized scaffold was observed by gross, toluidine blue staining, HE staining, scanning electron microcope (SEM), Alcian blue staining, and immunohistochemisty staining to evaluate the structure and essential component of extracellular maxtix (ECM) in the scaffold. Results Tissue engineered scaffold based on decellularized whole heart ECM was successfully prepared, which maintained not only the gross morphology of the heart, but also the intact vascular structure and ultrastructural conformation that certified by toluidine blue staining, HE staining, and SEM analyses. Alcian blue staining and immunohistochemisty staining showed that the essential components of ECM, such as collagen type I, glycosaminoglycan, fibronectin, and Laminin were remained in decellularized whole heart matrix. Conclusion The decellularized whole heart ECM prepared by method mentioned can maintain the intact structure of rat heart and basic compositions of extracellular matrices, so it could be suitable for further studies of tissue engineered scaffolds for whole heart reconstruction.