Porous graphene oxide (GO) nanocomposite as scaffold has attracted increasing attention in bone tissue engineering recently. In this study, GO nanosheets was modified by 2,2′-(ethylenedioxy)-diethnethiol (EDDET), and dithiol-modified GO (DT-GO) nanosheets were obtained. The results confirmed that GO nanosheets were cross-linked by EDDET, meanwhile, the distance between GO layers reduced after modification. Next, DT-GO nanosheets were further incorporated into alginate hydrogels to fabricate DT-GO/alginate (DT-GA) nanocomposite as scaffold. The prepared DT-GA nanocomposite behaved the laminar network morphology with interconnected porous structure confirmed by SEM analysis. In addition, the DT-GA nanocomposite with the concentration of DT-GO nanosheets at 16.7% showed the highest porosity value and lowest compressive strength. Furthermore, the bone marrow derived mesenchymal stem cells (BMSCs) showed a good proliferation on DT-GA nanocomposite, demonstrated that prepared nanocomposite had a good cytocompatibility, which was identified by CCK-8 assay and fluorescent microscopy images. Lastly, ALP activity analysis certified that BMSCs seeded on DT-GA nanocomposite could differentiate into osteoblastic phenotype. Above results suggest that the dithiol-modified GO/alginate nanocomposite has the potential to be applied in bone tissue engineering.