Organic nonvolatile transistor-type memory (ONVM) devices are developed using self-assembled nanowires of n-type semiconductor, N,N′-bis(2-phenylethyl)-perylene-3,4:9,10-tetracarboxylic diimide (BPE-PTCDI). The effects of nanowire dimension and silane surface treatment on the memory characteristics are explored. The diameter of the nanowires is reduced by increasing the non-solvent methanol composition, which led to the enhanced crystallinity and high field-effect mobility. The BPE-PTCDI nanowires with small diameters induce high electrical fields and result in a large memory window (the shifting of the threshold voltage, ΔVth). The ΔVth value of BPE-PTCDI nanowire based ONVM device on the bare substrate can reach 51 V, which is significantly larger than that of thin film. The memory window is further enhanced to 78 V with the on/off ratio of 2.1 × 104 and the long retention time (104 s), using a hydrophobic surface (such as trichloro(phenyl)silane-treated surface). The above results demonstrate that the n-type semiconducting nanowires have potential applications in high performance non-volatile transistor memory devices.