In this study, we fabricated a modified biomaterial based on chitosan and gelatin, which is an intrinsic hydrophilic membrane for oil–water separation to clean water contamination by oil. Modification of the membrane with a non-toxic natural crosslinker, genipin, significantly enhanced the stability of the biopolymer membrane in a water-based medium towards an eco-friendly environment. The effects of various compositions of genipin-crosslinked chitosan–gelatin membrane on the rheological properties, thermal stability, and morphological structure of the membrane were investigated using a dynamic rotational rheometer, thermogravimetry analysis, and chemical composition by attenuated total reflectance spectroscopy (ATR). Modified chitosan–gelatin membrane showed completely miscible blends, as determined by field-emission scanning electron microscopy, differential scanning calorimetry, and ATR. Morphological results showed membrane with establish microstructure to further experiment as filtration product. The membranes were successfully tested for their oil–water separation efficiencies. The membrane proved to be selective and effective in separating water from an oil–water mixture. The optimum results achieved a stable microporous structure of the membrane (microfiltration) and a separation efficiency of above 98%. The membrane showed a high permeation flux, generated as high as 698 and 420 L m−2 h−1 for cooking and crude oils, respectively. Owing to its outstanding recyclability and anti-fouling performance, the membrane can be washed away easily, ensuring the reusability of the prepared membrane.