Choice of appropriate biomaterial is a key factor for the success of recombinant human bone morphogenetic protein (rhBMP)-2 therapy. Inspired by osteogenic cell-differentiating and osteoclast-suppressing capabilities of alendronate (ALN), we manufactured a composite type of ALN-loaded collagen sponge (ALN-CS), which controls the early detrimental effect of high-dose rhBMP-2. This study aimed to evaluate ALN-CS as a high-dose rhBMP-2 carrier by investigating its initial biomolecular effect and efficacy on intramembranous ossification at 1, 4, 8, and 24 weeks using a rat calvarial defect model compared with nonloaded CS. The in vitro rhBMP-2 release in the ALN-CS showed a low initial burst and steady release phase during the rest period despite lack of calcium compared with that in CS alone. ALN release showed the same tendency as rhBMP-2 release. In vitro characterization showed that osteoblast differentiation and mineralization of mesenchymal stromal cells were more enhanced with ALN-CS. The ALN-CS-BMP group showed higher expression of bone-forming and -resorbing markers in vivo than the CS-BMP group after the first 7 days, which might be attributable to the relatively large amount of rhBMP-2 remaining. However, osteoclast activation in the ALN-CS-BMP group was significantly reduced compared with the CS-BMP group. Radiological and histological analyses revealed that ALN-CS-BMP promoted early and dense ossification at the initial defect, with 100% greater bone mass, 20% greater bone density, and less fatty marrow tissue than CS-BMP, which continued during the whole healing period. However, CS or ALN-CS alone failed to show complete defect closure even at the 24-week healing interval. Our results demonstrate that ALN-CS has remarkable advantages over CS alone in high-dose BMP-2 delivery, with potent suppression of resorption, early and dense ossification at the target area with less fatty marrow formation, and continuation of bone quality over the long term, which highlights its great clinical potential as a rhBMP carrier for bone regeneration at intramembranous ossification sites.