Macroscopic mechanical properties of porous PHBV bone TE scaffolds have been well studied. However, their mechanical behavior at microscopic level has yet to be explored. In this study, the micro-mechanical behavior of a PHBV bone scaffold under compression was investigated using a numerical method that combines micro-computed tomography (μ-CT) and finite element analysis (FEA). It was found that the use of a linear-elastic model resulted in an overestimation of the stiffness of the scaffold, whereas a more realistic estimation of the scaffold's deformation behavior was obtained by utilizing a bilinear material model. The onset of plastic deformation occurred in the very early stage of loading resulting in significantly reduced stiffness of the scaffold. The non-uniform and arbitrary microstructure of the scaffold led to a heterogeneous stress distribution within the porous construct, which was subjected to a mixture of compressive and tensile stresses. Nevertheless, the resultant stress contours showed that the scaffold experienced primarily elastic deformation when it was loaded up to 0.003 strain, while localized plastic deformation occurred at sharp corners and necked regions of the micro-struts. The scaffold expanded slightly in the horizontal direction as it was compressed and the change in geometries of pores within the scaffold was insignificant. The proposed method provides a valuable tool to study the localized mechanical behavior of bone scaffolds in micrometer scale with arbitrary porous architecture. This approach could prove highly useful for guiding the fabrication of scaffolds that have anatomy specific mechanical properties and porous architecture.