Carbon capture using membrane gas absorption was limited by membrane wetting. In this work, superhydrophobic poly(vinylidene fluoride) (PVDF) membrane contactors were developed through 3D-imprinting and nanoparticle incorporation. Membranes were cast on woven support before phase inversion in a water bath to imprint the micro-roughness. The low-cost and biocompatible calcium carbonate (CaCO3) nanoparticles were blended into PVDF dope solution to build the hierarchical structure. The nanoparticles were premodified using stearic acid to reduce surface energy or removed using ethylenediaminetetraacetic acid for achieving nanotemplating. The presence of CaCO3 nanoparticles could be observed using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The membrane hydrophobicity, pore size, and porosity were significantly improved due to the addition of CaCO3 and stearic acid-modified CaCO3 (SA-CaCO3). Removing CaCO3 nanoparticles enlarged the pore size greatly but affected the surface hydrophobicity slightly. The PVDF membrane incorporated with SA-CaCO3 achieved a CO2 permeation flux as high as 1.86 ± 0.05 × 10−2 mol m−2 s−1 and only showed slight changes in surface hydrophobicity after being immersed in amine solution for 50 h.