Because of the shortage of donors, alveolar stem cells transplantation is under development as an important and promising treatment for end-stage lung disease. Currently, the acquisition of functional lung cells is mostly performed by two dimensional (2D) culture and suffers from low directed differentiation efficiency. It is particularly critical to replicate the three dimensional (3D) growth of lung cells, as cells grow in 3D microenvironment in vivo. In this work, we develop a 3D biomimetic composite hydrogel system based on the in situ crosslinking of the synthetic polymer 4 arm acrylated-poly(ethylene glycol) (4PEG-AC), the thiolated natural polymer hyaluronic acid (HA-SH), and the thiolated polypeptide (GSE4-SH) via a Michael-type “click” reaction under physiological conditions at pH 7.8. The PEG/HA/GSE4 hydrogel with a sheer modulus of 104.1 ± 9.9 Pa was used for 3D growth of bone marrow mesenchymal stem cells (BMSCs), displaying excellent biocompatibility. Covalent conjugation of GSE4 peptide in hydrogel promoted the differentiation of BMSCs into alveolar epithelial type 2 cells (AEC2s) with a AEC2s-differentiation rate of 58.6 ± 3.3%. Overall, this study provides a suitable 3D biomimetic platform to enable the efficient differentiation of stem cells into lung cells for lung tissue engineering.