A clear understanding of carbon fiber (CF) microstructure is necessary for the development of high strength CFs. Here, we present an atomistic approach for generating and characterizing realistic mi- crostructures of CFs. Large-scale reactive molecular dynamics simulations are used to generate a set of distinct CF microstructures. Comprehensive characterization of the simulated microstructures is enabled by the development of a suite of computational structural analysis tools capable of evaluation of hy- bridization states of carbon atoms, populations and orientations of individual carbon rings, degree of graphitization, and pore size distribution. The calculation of X-ray diffraction profiles provides a direct link between the structural features of simulated samples and experimental data available for CFs. The CF generation algorithm is shown to produce microstructures with experimental densities and with structural characteristics matching those of PAN-based CFs. The key structural features affecting the properties of CFs, such as the relative fractions of graphitic, turbostratic and amorphous micro- constituents, degree of alignment, pore size distributions, and chemical cross-linking can be effectively controlled in simulations, thus enabling efficient exploration of structureeproperties relationships in CFs. The capabilities of the developed approach are illustrated by performing computational analysis of the mechanical deformation and fracture of CFs under axial tensile loading.