In this study, both nanoclay and COOH-functionalized multi-walled carbon nanotubes (MWCNTs) were mixed with SC-15 epoxy resin system, individually as well as together, referred as binary nanoparticles. Resulting nanocomposite was used to prepare multi-phase carbon/epoxy composites. Composites were characterized for their thermal, thermo-mechanical, tensile, and flexural properties. Failure modes of tensile and flexural samples were determined through optical and scanning electron microscopy. Properties of multi-phased nanocomposites were compared with those of carbon/epoxy composites with no nanoparticles, referred to as neat samples. While all nanophased samples exhibited better properties compared to the neat samples, composites with binary nanoparticles exhibited the best properties. Their flexural strength and modulus increased about 30 and 31%, respectively. Tensile strength, modulus, and strain to failure increased by about 28, 27, and 40%, respectively. In addition, they exhibited about 40, 44, and 19% improvement in storage modulus, loss modulus, and glass transition temperature, respectively. Coefficient of thermal expansion (CTE), when measured through thickness, decreased by about 15 and 40%, before and after glass transition temperature, respectively. Morphological and microscopic analyses exhibit higher interfacial adhesion of resin and fibers when matrix is modified with nanoparticles.