Collagen hydrogels were considered as favourable scaffolding for tissue engineering. It was demonstrated that cytokines and siRNAs could be efficiently retained by collagen hydrogels for controlled release thereby enhancing their bioactivities. Basic fibroblast growth factor (bFGF) was a stimulator for osteogenic differentiation of mesenchymal stem cells (MSC), and PPARγ was a key regulator in MSC osteogenic differentiation. However, whether bFGF and PPARγ could play synergetic roles within a 3D matrix to promote MSC osteogenic differentiation was unknown. In the study, bFGF and PPARγ targeting siRNAs were incorporated into collagen hydrogels for MSC cultivation. Their optimal concentrations in collagen hydrogels were determined. The capacity of bFGF/siRNA-carrying hydrogels in supporting osteogenic differentiation of MSCs was systematically evaluated with multimodality of methods, including flow cytometry, quantitative real-time PCR, Western Blotting, as well as ALP activity and calcium content determination. We demonstrated in 3D collagen hydrogel that both bFGF and siRNA molecules were efficiently retained, strengthening their effects on the incorporated MSCs. Osteogenic analysis demonstrated that the in-situ forming hydrogels carrying bFGF and siRNAs potently promoted osteogenic differentiation of incorporated MSCs, significantly superior to pure collagen and bFGF-carrying collagen. Thus, collagen hydrogels functionalized with bFGF and PPARγ targeting siRNAs may be promising in bone tissue engineering.