The influences of pore sizes and surface modifications on biomechanical properties and biocompatibility (BC) of porous tracheal scaffolds (PTSs) fabricated by polycaprolactone (PCL) using 3D printing technology. The porous grafts were surface‐modified through hydrolysis, amination, and nanocrystallization treatment. The surface properties of the modified grafts were characterized by energy dispersive spectroscopy (EDS) and scanning electron microscopy (SEM). The materials were cocultured with bone marrow mesenchymal stem cells (BMSCs). The effect of different pore sizes and surface modifications on the cell proliferation behavior was evaluated by the cell counting kit‐8 (CCK‐8). Compared to native tracheas, the PTS has good biomechanical properties. A pore diameter of 200 μm is the optimum for cell adhesion, and the surface modifications successfully improved the cytotropism of the PTS. Allogeneic implantation confirmed that it largely retains its structural integrity in the host, and the immune rejection reaction of the PTS decreased significantly after the acute phase. Nano‐silicon dioxide (NSD)‐modified PTS is a promising material for tissue engineering tracheal reconstruction. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 360–370, 2019.