Polyether ether ketone (PEEK) is a high-performance, semi-crystalline thermoplastic that is used in a wide range of engineering applications, including some structural components of aircraft. The design of new PEEK-based composite materials can be greatly facilitated with a precise understanding of the multiscale structure and behavior of semi-crystalline PEEK. Molecular Dynamics (MD) modeling can efficiently predict the response of single-phase polymers at the nanometer length scale, and micromechanics can be used to predict the bulk-level properties of mull-phase materials based on the microstructure. In this study, MD modeling was used to predict the mechanical response of the amorphous and crystalline phases of PEEK. Employing the MD simulation results as input, the hierarchical microstructure of PEEK, which combines these two phases, was modeled using NASA's micromechanics MSGMC (Mull-Scale Generalized Method of Cells) code. The predicted bulk mechanical properties of semi-crystalline PEEK agree well with the scientific literature data, thus validating the multiscale modeling approach. Thus, the proposed multiscale modeling method can be used to accurately and efficiently predict the mechanical response of other micro-structurally complex polymer systems.