Porous polydimethylsiloxane (PDMS) membrane is a crucial element in organs-on-chips fabrication, supplying a unique substrate that can be used for the generation of tissue-tissue interfaces, separate co-culture, biomimetic stretch application, etc. However, the existing methods of through-hole PDMS membrane production are largely limited by labor-consuming processes and/or expensive equipment. Here, we propose an accessible and low-cost strategy to fabricate through-hole PDMS membranes with good controllability, which is performed via combining wet-etching and spin-coating processes. The porous membrane is obtained by spin-coating OS-20 diluted PDMS on an etched glass template with a columnar array structure. The pore size and thickness of the PDMS membrane can be adjusted flexibly via optimizing the template structure and spinning speed. In particular, compared to the traditional vertical through-hole structure of porous membranes, the membranes prepared by this method feature a trumpet-shaped structure, which allows for the generation of some unique bionic structures on organs-on-chips. When the trumpet-shape faces upward, the endothelium spreads at the bottom of the porous membrane, and intestinal cells form a villous structure, achieving the same effect as traditional methods. Conversely, when the trumpet-shape faces downward, intestinal cells spontaneously form a crypt-like structure, which is challenging to achieve with other methods. The proposed approach is simple, flexible with good reproducibility, and low-cost, which provides a new way to facilitate the building of multifunctional organ-on-chip systems and accelerate their translational applications.