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Crystallization and phase separation in the melt in semicrystalline block copolymers (BCPs) compete in defining the final solid state structure and morphology. In crystalline–crystalline di-block copolymers the sequence of crystallization of the two blocks plays a definitive role. In this work we show that the use of epitaxial crystallization on selected crystalline substrates allows achieving of a control over the crystallization of the blocks by inducing crystal orientations of the different crystalline phases and a final control over the global morphology. A sample of polyethylene-block-syndiotactic polypropylene (PE-b-sPP) block copolymers has been synthesized with a stereoselective living organometallic catalyst and epitaxially crystallized onto crystals of two different crystalline substrates, p-terphenyl (3Ph) and benzoic acid (BA). The epitaxial crystallization on both substrates produces formation of highly ordered morphologies with crystalline lamellae of sPP and PE highly oriented along one direction. However, the epitaxial crystallization onto 3Ph should generate a single orientation of sPP crystalline lamellae highly aligned along one direction and a double orientation of PE lamellae, whereas BA crystals should induce high orientation of only PE crystalline lamellae. Thanks to the use of the two selective substrates, the final morphology reveals the sequence of crystallization events during cooling from the melt and what is the dominant event that drives the final morphology. The observed single orientation of both crystalline PE and sPP phases on both substrates, indeed, indicates that sPP crystallizes first onto 3Ph defining the overall morphology and PE crystallizes after sPP in the confined interlamellar sPP regions. Instead, PE crystallizes first onto BA defining the overall morphology and sPP crystallizes after PE in the confined interlamellar PE regions. This allows for discriminating between the different crystalline phases and defining the final morphology, which depends on which polymer block crystallizes first on the substrate. This work also shows that the use of epitaxial crystallization and the choice of suitable substrate offer a means to produce oriented nanostructures and morphologies of block copolymers depending on the composition and the substrates.