Honeycomb-patterned films (HPFs) of Au nanoparticles (Au NPs) with pore size controlled by varying the quantity of Au NPs or using modified agents of different mercaptans (C14H29SH, C16H33SH, and C18H37SH) were prepared. The strength of the HPFs containing Au NPs can be enhanced because of the addition of polymers including polystyrene, poly(L-lactic acid), and poly(methyl methacrylate-co-ethyl acrylate). With an increase in the amount of polymer and the number of Au NPs or the chain length of the modified agents, the pore size of HPFs decreases, indicating that the pore size can be well controlled by adjusting the above factors. Interestingly, HPFs with elliptical pores that were created by the direction of the air flow were observed. The pore diameter on the outer rim is smaller than that in the center, which should be because of the subordinate evaporation of the solvent in the center. Sponge structures were observed in the cross sections of the walls of HPFs, which should be produced by microphase separation. The HPFs consisting of Au NPs with controllable pore size exhibited stronger surface-enhanced Raman scattering. We believe that the HPFs composed of metal NPs such as Au, Ag, and Cu are exploited in multispectral scanners, nanophotons, and sensors.