It is highly desired to own antibacterial function and sufficient mechanical properties for bone scaffolds. Introducing graphene oxide (GO) could increase the mechanical properties while nano Ag could impart antibacterial function for polymer scaffolds, but either GO or nano Ag easily forms aggregates, hindering the full play of the efficiency. In this study, we proposed a co-dispersing GO-Ag nanosystem where GO nanosheets loaded Ag nanoparticles while Ag nanoparticles intercalated into the interlayers of GO nanosheets, in which GO nanosheets and Ag nanoparticles supported each other, hence achieving a co-dispersion. The co-dispersing GO-Ag nanosystem was introduced into polymer scaffolds, prepared by additive manufacturing technology. The results indicated that the GO-Ag nanosystem showed a synergistic effect on antibacterial action via combining the capturing effects of GO nanosheets and the killing effects of Ag; the scaffold containing 1 wt% GO-1 wt% Ag showed a bacterial inhibition rate more than 95%. Moreover, GO and Ag showed another synergistic effect on mechanically enhancing the scaffolds as the co-dispersing nanosystem increased the efficiency of the stress transfer in the matrix; the compressive strength and modulus were increased by 102 and 82%, respectively. Besides, the scaffold showed good cytocompatibility. This study suggested that the antibacterial and mechanically reinforced scaffolds may have potential applications in bone tissue engineering.