To evaluate the efficacy of 3D-printed scaffolds that were osteoinductively functionalized with a bone morphogenetic protein 2 (BMP-2)-incorporated biomimetic calcium phosphate particles (BMP-2-inc. BpNcCaP)/hyaluronic acid (HA) composite gel in vertical bone augmentation in beagle dogs. Four Beagle dogs were used in this study. Three months after the extraction of 1st, 2nd, 3rd, and 4th premolars at both sides of the lower jaws of Beagle dogs, one or two critical-size vertical bone defects (4 mm vertical bone defect without buccal and lingual bone) on each sidewere surgically created. The defects were randomly subjected to the following groups: (1) Control (without bone-defect-filling materials); (2) 3D scaffold; (3) BMP2-inc. BpNcCaP/HA-functionalized 3D scaffold. Six weeks post-surgery, samples were harvested and subjected to micro-CT and histomorphometric analyses. The struts of the BMP2-inc. BpNcCaP/HA-func. 3D scaffold were covered by a thick layer of cemented irregular particles with an average pore size at 327 ± 27 μm. The BpNcCaP/HA-func. 3D scaffold group bore significantly higher bone volume, bone volume fraction, trabecular number, trabecular thickness, bone mineral density, connectivity density, and bone volumes in three directions (mesiodistal, buccolingual, and apicocoronal) when compared with the groups of Control and 3D scaffold. Moreover, the BMP2-inc. BpNcCaP/HA-func. 3D scaffold group bore significantly lower trabecular separation and exhibited significantly higher bone-to-scaffold contact percentage and newly formed bone area percentage within pores in comparison with 3D scaffold. BMP2-inc. BpNcCaP/HA-func. 3D scaffold dramatically enhanced vertical alveolar bone augmentation, which suggests a promising application potential of BMP2-inc. BpNcCaP/HA-func. 3D scaffold in dental clinic.