Current efforts had been made to undertake a three-dimensional (3-D) reverse transfection of bone marrow-derived mesenchymal stem cells (BM-MSCs) in PLGA scaffolds. As a kind of multipotent stem cells, BM-MSCs show great potential and tremendous capacity in the gene transfection field and PLGA 3-D scaffold has been shown to be a biomaterial that provides structural support to cells proliferation and tissue engineering. The objective of this study was to assess the transfection efficiency of BM-MSCs with a 3-D reverse transfection method by using PLGA scaffold and observe the SEM photographs of BM-MSCs cultured on PLGA scaffold. BM-MSCs were cultured in 3-D PLGA scaffold which was incorporated with pullulan-spermine/pGL3. It was shown that the gene expression duration of BM-MSCs transfected using 3D reverse method with pullulan-spermine/DNA in the presence of serum maintained 12 days at high levels as compared with the plasmid DNA in medium, and scanning electronic microscopy (SEM) photographs of BM-MSCs cultured on PLGA scaffold exhibited robust cell attachment and viability when cultured in PLGA scaffold in vitro. This study demonstrates that the 3-D reverse transfection method of BM-MSCs using PLGA scaffold could achieve long gene expression in a relatively high level, therefore this transfection system is promising in gene transfection and tissue engineering.