In this paper, polyacrylonitrile (PAN) nanofibrous membranes (NFMs) were prepared by electrospinning technology. Copper (Cu) or/and zinc (Zn) nanoparticles (NPs) were deposited on the surface of PAN NFMs by spark ablation technology to fabricate a surface structure with antibacterial and hydrophobic properties. The deposition of NPs was controlled using current, voltage, carrier gas flow rate, and load time. The fabricated NFMs were characterized by FE-SEM, EDX, XRD, and water contact angle. Moreover, the antibacterial properties of the fabricated NFMs were studied using the agar-diffusion test method. The results showed that Cu, or/and Zn NPs successfully deposited on the surface of PAN NFMs, which improved the hydrophobicity by increasing the water contact angle from 46° to 128°, 130°, and 136°, respectively. Besides, the Zn@PAN NFMs sample was showed good antibacterial property against both Gram-negative and Gram-positive bacterial strains. Overall, the NPs@PAN NFMs based spark ablation technology might afford an easy-to-operated design pattern for constructing potential materials for water treatment applications.