Substitution by artificial ovary is a promising approach to restore ovarian function, and a decellularized extracellular matrix can be used as a supporting scaffold. However, biomimetic ovary fabrication and immunogenicity requires more investigation. In this study, we proposed an effective decellularization protocol to prepare ovarian scaffolds, which were characterized by few nuclear substances and which retained the extracellular matrix proteins. The ovarian tissue shape and 3-dimensional structure were well-preserved after decellularization. Electron micrographs demonstrated that the extracellular matrix fibers in the decellularized group had similar porosity and structure to those of native ovaries. Semi-quantification analysis confirmed that the amount of extracellular matrix proteins was reduced, but the collagen fiber length, width, and straightness did not change significantly. Granulosa cells were attached and penetrated into the decellularized scaffold and exhibited high proliferative activity with no visible apoptotic cells on day 15. Follicle growth was compromised on day 7. The implanted artificial ovaries did not restore endocrine function in ovariectomized mice. The grafts were infiltrated with immune cells within 3 days, which damaged the artificial ovary morphology. The findings suggest that immune rejection plays an important role when using artificial ovaries.