A bioactive paradigm is required to promote osseointegration of implant materials. Here, a protamine/alginate/bone morphogenic protein 2 (BMP2) biofunctionalized composite coating was created on nanopolymorphic titanium (Ti) surfaces to promote the osseointegration of Ti implants. Alkali and heat (AH) treatment was used to make porous Ti implants (TiAH) with a superhydrophilic and negatively charged surface, which facilitates the adsorption of a positively charged protamine/alginate/protamine (TiAH-Pro/Alg/Pro) coating. Biofunctionalization of the substrate was achieved via further immobilization of exogenous BMP2 (TiAH-Pro/Alg/Pro-BMP2). The results indicated the successful deposition of Pro/Alg/Pro coatings onto porous TiAH substrates. In addition, the initial burst release of the adsorbed protein was effectively dampened by the TiAH-Pro/Alg/Pro coating, allowing uniform protein distribution and sustained biomolecule release. In comparison with the pristine Ti, the three modified substrates showed good cytocompatibility and promoted cell adhesion in the initial period. The adherent cells on the TiAH-Pro/Alg/Pro surface and TiAH-Pro/Alg/Pro-BMP2 substrate exhibited distinct shapes compared to those on the pristine Ti and TiAH surfaces. Moreover, TiAH-Pro/Alg/Pro-BMP2 significantly improved the in vitro osteogenic differentiation of MC3T3-E1 cells and enhanced the osseointegration in the in vivo rat model. Such facilitative effects may be achieved by activating integrins and the BMP/Smad signaling pathway. This study highlights the potential of combining inorganic with organic surface modifications for accelerating the osseointegration of implant materials.