Atomic layer deposition (ALD) is a unique tool for conformally depositing inorganic thin films with precisely controlled thickness at nanoscale. Recently, ALD has been used in the manufacture of inorganic thin films using a three-dimensional (3D) nanonetwork structure made of polymer as a template, which is pre-formed by advanced 3D nanofabrication techniques such as electrospinning, block-copolymer (BCP) lithography, direct laser writing (DLW), multibeam interference lithography (MBIL), and phase-mask interference lithography (PMIL). The key technical requirement of this polymer template-assisted ALD is to perform the deposition process at a lower temperature, preserving the nanostructure of the polymer template during the deposition process. This review focuses on the successful cases of conformal deposition of inorganic thin films on 3D polymer nanonetworks using thermal ALD or plasma-enhanced ALD at temperatures below 200 °C. Recent applications and prospects of nanostructured polymer–inorganic composites or hollow inorganic materials are also discussed.