Periodontal tissue regeneration is a major challenge in tissue engineering due to its regenerated environment complexity. It aims to regenerate not only the supporting alveolar bone and cementum around teeth but also the key connecting periodontal ligament. Herein, a constructed aligned porous hydrogel scaffold carrying cells based on chitosan (CHI) and oxidized chondroitin sulfate (OCS) treated with a freeze-casting technique was fabricated, which aimed to induce the arrangement of periodontal tissue regeneration. The microscopic morphology and physical and chemical properties of the hydrogel scaffold were evaluated. The biocompatibilities with periodontal ligament stem cells (PDLSCs) or gingival-derived mesenchymal stem cells (GMSCs) were verified, respectively, by Live/Dead staining and CCK8 in vitro. Furthermore, the regeneration effect of the aligned porous hydrogel scaffold combined with PDLSCs and GMSCs was evaluated in vivo. The biocompatibility experiments showed no statistical significance between the hydrogel culture group and blank control ( > 0.05). In a rat periodontal defect model, PDLSC and GMSC hydrogel experimental groups showed more pronounced bone tissue repair than the blank control ( < 0.05) in micro-CT. In addition, there was more tissue repair ( < 0.05) of PDLSC and GMSC hydrogel groups from histological staining images. Higher expressions of OPN, Runx-2, and COL-I were detected in both of the above groups via immunohistochemistry staining. More importantly, the group with the aligned porous hydrogel induced more order periodontal ligament formation than that with the ordinary hydrogel in Masson's trichrome analysis. Collectively, it is expected to promote periodontal tissue regeneration utilizing an aligned porous hydrogel scaffold combined with PDLSCs and GMSCs (CHI-OCS-PDLSC/GMSC composite), which provides an alternative possibility for clinical application.