In this study, the morphology of the nanostructures is evaluated on the surface characterization and performance of the polyacrylonitrile (PAN) ultrafiltration mixed matrix membranes (MMM). To this end, silica nanoparticles (NPs) such as spherical (SiO2) and hexagonal mesoporous (MCM‐41) with high hydrophilicity were incorporated at 0.5, 1, and 2 wt%. Attenuated total reflectance‐Fourier transform infrared analysis illustrated the placement of NP on the surface of the MMM. Atomic force microscopy studies also showed that SiO2 NP added to PAN exhibited a smoother surface than MCM‐41 NP. Field‐emission scanning electron microscope analysis of the MMM identified that all membranes are composed of a finger‐like porous structure. Contact angle measurements indicate that the morphology of the NPs has no significant effect on MMM hydrophilicity. Moreover, the performance of the MMM was evaluated, and regardless of NP morphology, the MMM showed better permeate flux with increased loading. A higher pure water flux was observed in the PAN‐MCM41‐1% membrane (237 L/m2 h), possibly because of inherent porosity and high hydrophilicity of MCM‐41 compared to SiO2 NP. Further, the PAN‐SiO2‐1% membrane exhibited superior antifouling properties due to a lower surface roughness. The present studies reveal that the morphology of the NP greatly influence on the structure, permeation, and antifouling properties of PAN membranes.