Globally, one of the most common tissue transplantation procedures is bone grafting. Lately, we have reported the development of polymerized high internal phase emulsions (PolyHIPEs) made of photocurable polycaprolactone (4PCLMA) and shown their potential to be used as bone tissue engineering scaffolds in vitro. However, it is essential to evaluate the in vivo performance of these scaffolds to investigate their potential in a clinically more relevant manner. Therefore, in this study, we aimed to compare in vivo performances of macroporous (fabricated using stereolithography), microporous (fabricated using emulsion templating), and multiscale porous (fabricated using emulsion templating and perforation) scaffolds made of 4PCLMA. Also, 3D-printed macroporous scaffolds (fabricated using fused deposition modeling) made of thermoplastic polycaprolactone were used as a control. Scaffolds were implanted into a critical-sized calvarial defect, animals were sacrificed 4 or 8 weeks after implantation, and the new bone formation was assessed by micro-computed tomography, dental radiography, and histology. Multiscale porous scaffolds that include both micro- and macropores resulted in higher bone regeneration in the defect area compared to only macroporous or only microporous scaffolds. When one-grade porous scaffolds were compared, microporous scaffolds showed better performance than macroporous scaffolds in terms of mineralized bone volume and tissue regeneration. Micro-CT results revealed that while bone volume/tissue volume (Bv/Tv) values were 8 and 17% at weeks 4 and 8 for macroporous scaffolds, they were significantly higher for microporous scaffolds, with values of 26 and 33%, respectively. Taken together, the results reported in this study showed the potential application of multiscale PolyHIPE scaffolds, in particular, as a promising material for bone regeneration.