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Graphene-based nanocomposites such as graphene oxide (GO) and nanoparticle-decorated graphene with demonstrated excellent physicochemical properties have worthwhile applications in biomedicine and bioengineering such as tissue engineering. In this study, we fabricated gold nanoparticle-decorated GO (GO-Au) nanocomposites and characterized their physicochemical properties using UV-Vis absorption spectra, FTIR spectra, contact angle analyses, and free radical scavenging potential. Moreover, we investigated the potent applications of GO-Au nanocomposites on directing mesenchymal stem cells (MSCs) for tissue regeneration. We compared the efficacy of as-prepared GO-derived nanocomposites including GO, GO-Au, and GO-Au (×2) on the biocompatibility of MSCs, immune cell identification, anti-inflammatory effects, differentiation capacity, as well as animal immune compatibility. Our results showed that Au-deposited GO nanocomposites, especially GO-Au (×2), significantly exhibited increased cell viability of MSCs, had good anti-oxidative ability, sponged the immune response toward monocyte-macrophage transition, as well as inhibited the activity of platelets. Moreover, we also validated the superior efficacy of Au-deposited GO nanocomposites on the enhancement of cell motility and various MSCs-derived cell types of differentiation including neuron cells, adipocytes, osteocytes, and endothelial cells. Additionally, the lower induction of fibrotic formation, reduced M1 macrophage polarization, and higher induction of M2 macrophage, as well as promotion of the endothelialization, were also found in the Au-deposited GO nanocomposites implanted animal model. These results suggest that the Au-deposited GO nanocomposites have excellent immune compatibility and anti-inflammatory effects in vivo and in vitro. Altogether, our findings indicate that Au-decorated GO nanocomposites, especially GO-Au (×2), can be a potent nanocarrier for tissue engineering and an effective clinical strategy for anti-inflammation.