A study of the morphology of diblock copolymers composed of two crystalline blocks of isotactic polypropylene (iPP) and polyethylene (PE) is shown. The samples form phase-separated structures in the melt because of the incompatibility between iPP and PE blocks. Cylindrical PE microdomains are visible at room temperature in the sample with a PE volume fraction of 26%, rapidly quenched from the melt in liquid nitrogen. In the quenched sample, PE crystallizes inside the PE cylindrical microdomains, whereas crystals of iPP are not visible in the iPP domains because the quenching prevents crystallization of the lamellar alpha form. Less rapid cooling of the melt produces, instead, breakout crystallization, where the phase-separated structure of the melt is destroyed by the slow crystallization of the alpha form of iPP and of PE. The succession of crystallization of iPP and PE and the resulting final morphology have been analyzed by inducing selective and different orientations of iPP and PE crystals through epitaxial crystallization onto the benzoic acid (BA) crystal substrate. Epitaxy produces oriented crystallization of iPP and PE, with a unique alignment of PE lamellar crystals and a double orientation of iPP crystals on to the (001) exposed face of BA. Epitaxy destroys the phase-separated structure of the melt and induces the formation of ordered lamellar nanostructures with alternated layers of iPP and PE, whose orientation is defined by the alignment of PE or iPP crystals, which, in turn, is determined by epitaxy. The results indicate that crystalline block copolymers offer the opportunity to create nanoscale patterns on thin films and improve the possibility of controlling the microstructure of block copolymers and the alignment of microdomains by controlling the crystallization process.