We aimed to replicate a nano-scale mesh structure of a hydrogel by assembling silica nanoparticles densely in the nano-scale mesh structure. A pre-gel aqueous solution of N-isopropyl acrylamide (NIPAM) and sol-gel-derived silica sol prepared from tetraorthoethyl silicate (TEOS) were mixed to carry out the polymerization/cross-linking and silanol condensation. A homogeneous hybrid of poly-NIPAM gel and silica was successfully obtained. After removing the poly-NIPAM gel by calcination at 873 K in air, electron microscope observations revealed that the poly-NIPAM gel was replicated as network-or channel-like nanopores. The pore size distribution obtained by nitrogen adsorption/desorption at 77 K showed qualitative agreement with the above results of the direct observation. Therefore, the nano-scale mesh-like structure of the NIPAM hydrogel was replicated to the channel-like nanopores. As the weight ratio of NIPAM gel to silica moiety was increased, the average pore size increased to approximately 10 nm, indicating the partial nano-scale segregation of NIPAM chains when its fraction was enhanced. A retarded drying process was revealed to be advantageous for the formation of bulk assembly of the nanoparticles. By minimizing the drying rate at the saturated moist condition, an optically transparent assembly of the silica nanoparticles could be prepared at a porosity up to about 75%. The retarded drying process also affected the size of the resultant nanopores because of the presence of residual volatile species like solvent water.