The regeneration of large-segment bone defects remains a significant clinical challenge due to their complex microenvironments. Three-dimensional (3D) printed polycaprolactone (PCL) scaffolds offer a potential solution but are limited by insufficient osteoinductivity. In this study, 3D-printed PCL/β-TCP composite scaffolds were pretreated with NaOH, followed by functionalization with bioactive COL and β‑TCP coatings. These modifications markedly improved scaffolds’ hydrophilicity without compromising mechanical integrity. In vitro studies with MC3T3-E1 cells demonstrated that the CS@TCP scaffolds significantly enhanced early osteogenic differentiation compared to C, CS, and CS@COL scaffolds, as indicated by the ALP activity experiment. In vivo evaluation using three different rabbit cranial defect models revealed superior new bone formation in the PTD groups compared to the FTD and Onlay groups, likely due to the increased vascularization and abundant endogenous stem cells in the PTD groups. Despite lower new bone formation in the Onlay groups, their bone integration advantages may benefit cosmetic surgery applications. This study aimed to investigate how β‑TCP surface modification synergizes with clinical application-specific microenvironments to maximize the regenerative potential of 3D-printed scaffolds, which provided crucial guidance for scaffold design in effective bone defect repair from different clinical scenarios.