Incorporating block copolymers into epoxy systems has emerged as a versatile and effective methodology not only to enhance their mechanical properties, but also as an intriguing strategy to design advanced materials with tailored properties. Knowledge of microphase separation mechanisms operating during the development of these materials is essential due to the straight relationship between block copolymer characteristics, epoxy system formulation, and curing conditions with the final nanodomain morphology. This chapter is focused on the thermodynamic and kinetic fundamentals describing microphase separation mechanisms by which the nanodomains are obtained. Moreover, key parameters affecting phase separation mechanisms and morphologies are discussed, explaining how different material properties can be tuned by controlling the nanostructure morphology.