This study aimed to investigate the feasibility of the nanostructured 3D poly(lactide-co-glycolide) (PLGA) constructs, which are loaded with dexamethasone (DEX) and growth factor embedded heparin/poly(L-lysine) nanoparticles via a layer-by-layer system, to serve as an effective scaffold for nucleus pulposus (NP) tissue engineering. Our results demonstrated that the microsphere constructs were capable of simultaneously releasing basic fibroblast growth factor and DEX with approximately zero order kinetics. The dual bead microspheres showed no cytotoxicity, and promoted the proliferation of the rat mesenchymal stem cells (rMSCs) by lactate dehydrogenase assay and CCK-8 assay. After 4 weeks of cultivation in vitro, the rMSCs-scaffold hybrids contained significantly higher levels of sulfated GAG/DNA and collagen type II than the control samples. Moreover, quantitative real time PCR analysis revealed that the expression of disc-matrix proteins including collagen type II, aggrecan, and versican in the rMSCs-scaffold hybrids was significantly higher than that in the control group, whereas the expression of osteogenic differentiation marker (collagen type I) was decreased. Taken together, these data indicate that Dex/bFGF PLGA microspheres could be used as a scaffold to improve the rMSCs growth and differentiating into NP like cells, and reduce the inflammatory response for IVD tissue engineering.