Biopolymer-based nanogels have great potential in the field of tissue regenerative medicine. In this work, a magnetic biopolymer nanogel via specific nucleobase pairing was developed for vectoring delivery of cell growth factors. The biopolymer based nanogels chitosan and heparin were established by the Watson-Crick base pairing between thymine and adenine via the hydrogen bonding. The magnetic biopolymer nanogels exhibit quick magnetic responsibility, which were fabricated by encapsulating super-paramagnetic iron oxide nanoparticles. The potential applications of this magnetic nanogel on vectoring delivery of cell growth factors were confirmed by adsorption and release behaviors of bone morphogenetic protein 2 (BMP-2). The existence of heparin made the nanogel achieve a high loading efficiency of BMP-2, and the vectoring delivery of BMP-2 could be easily controlled by the external magnetic field. In vitro cytotoxicity tests demonstrated that incorporation of BMP-2 into this biopolymer nanogel through binding with heparin showed high efficiency to promote MG-63 cells' viabilities, in particular under a magnetic field, which suggested a promising future for cartilage and bone regeneration applications.