Extraordinary superhydrophobic polycaprolactone (PCL) composite membranes with an alternated hierarchical micro-nano structure were designed by addition of SiO2 aerogel. The highest water contact angle (WCA) of 166.8 ± 1.5° was obtained when SiO2 aerogel content was 0.5% (PCL/SiO2-a0.5) in the PCL composite membrane, which was higher than other reported polymer-based membranes. SiO2 aerogel lowered PCL composite membrane's surface energy. The triple curvature structure composed of microspheres, nanospheres, and nanofibers produced on PCL/SiO2-a0.5 membranes endowed the excellent roughness of the surface. Also, the inner structure of the PCL/SiO2-a0.5 composite membrane composed of micro-nano spheres, nanofibers, and microfibers increased the porosity of the separation membrane, which would provide more adsorption space. The PCL/SiO2-a0.5 composite membrane as a separator for surfactant-stabilized emulsions of water-in-oil showed ultrahigh separation flux and efficiency. Meanwhile, the PCL/SiO2-a0.5 composite membrane had an outstanding chemical resistance, self-cleaning ability, and good reusability. The composite membranes reported in this work as eco-friendly separation materials possessed all these characters in oil/water separation. This research proposed a very simple method to design eco-friendly high-efficiency separators through the construction of the alternated micro-nano hierarchical structure.