In rechargeable lithium-ion batteries, understanding the atomic-scale mechanism of Li-induced structural evolution occurring at the host electrode materials provides essential knowledge for design of new high performance electrodes. Here, we report a new crystalline-crystalline phase transition mechanism in single-crystal Zn-Sb intermetallic nanowires upon lithiation. Using in situ transmission electron microscopy, we observed that stacks of atomic planes in an intermediate hexagonal (h-)LiZnSb phase are "shuffled" to accommodate the geometrical confinement stress arising from lamellar nanodomains intercalated by lithium ions. Such atomic rearrangement arises from the anisotropic lithium diffusion and is accompanied by appearance of partial dislocations. This transient structure mediates further phase transition from h-LiZnSb to cubic (c-)Li2ZnSb, which is associated with a nearly "zero-strain" coherent interface viewed along the [001]h/[111]c directions. This study provides new mechanistic insights into complex electrochemically driven crystalline-crystalline phase transitions in lithium-ion battery electrodes and represents a noble example of atomic-level structural and interfacial rearrangements.