With the continuous development of environmental protection and resource recycling demands, the development of bio-based separation membrane materials has increasingly attracted attention. Bio-based polyamide 56 (PA56), exhibiting excellent hydrophilicity, spinnability, and mechanical properties, is expected to complement and replace traditional separation membrane materials. In this study, the electrospinning preparation and structural control of PA56 nanofiber membranes were achieved through the optimization of PA56 content and mixed solvent ratios. The study found that when the PA56 content was 16 wt% and the formic acid to acetone ratio in the mixed solvent was 8:2, the nanofiber diameter distribution was the most uniform. Building on this, amino-functionalized modified silica (SiO2–NH2) nanoparticles were introduced to prepare PA56/SiO2–NH2 composite nanofiber membranes featuring a cobweb-like nanofiber network and micro-nodule structure. The effects of the addition of SiO2–NH2 nanoparticles on the morphology, structure, and properties of the fiber membranes were studied. The results indicate that the control of the mixed solvent ratio and the addition of SiO2–NH2 nanoparticles led to the formation of a cobweb-like nanofiber network and micro-nano nodular structure on the nanofiber surface, enhancing the hydrophilicity of PA56 nanofiber membranes. The M − 3 membrane with a nanoparticle addition amount of 0.8 wt% exhibited high hydrophilicity and underwater superoleophobic properties, achieving efficient separation of stable oil-in-water emulsions with a separation efficiency of 99.8 %. This work provides a new bio-based membrane material and its preparation method for treating oily wastewater using the membrane separation method.