Electrophoretic deposition (EPD) has been recognized as a promising large-scale film preparation technology for industrial application. Inspired by the conventional EPD method and the crystal diffusion growth strategy, we propose a modified electrophoretic-induced self-assembly deposition (EPAD) technique to control the morphologies of organic functional materials. Here, an ionic-type dye with a conjugated skeleton and strong noncovalent interactions, celestine blue (CB), is chosen as a module molecule for EPAD investigation. As expected, CB molecules can assemble into different nanostructures, dominated by applied voltage, concentration effect, and duration. Compared to a nanopillar layered packing structure formed by the traditional spin-coating method, the EPAD approach can produce a nanofiber structure under a fixed condition of 10 V/10 min. Intriguingly, a memristor device based on a pillar-like nanostructure exhibits WORM-type behavior, while a device based on nanofibers presents Flash memory performance. The assemble process and the memory mechanism are uncovered by molecular dynamics simulations and density-functional theory (DFT) calculations. This work endows the typical EPD technique with a fresh application scenario, where an in-depth study on the growth mechanism of nanofibers and the positive effect of unique morphologies on memristor performance are offered.