Nanoporous gold (NPG) has been reported to provide remarkable fluorescence enhancement of adjacent fluorophores due to the metal-enhanced fluorescence phenomenon (MEF), and the enhancement is related with the characteristic length of nanoporosity. To fully understand the effect of NPG on nearby fluorophores, it is desirable to study systems with well-defined metal-fluorophore distances. In this study we investigated the distance effect by using silica as the spacing layer between fluorophores and NPG. Originating from competition between plasmonic amplifying and metallic quenching, the dye molecule rhodamine 6G was best enhanced by 20-nm SiO2 coated nanoporous gold with the pore size of 36 nm, while the protein phycoerythrin was best enhanced by 15-nm SiO2 coated nanoporous gold with the pore size of 42 nm and the quantum dots were best enhanced by 20-nm SiO2 coated nanoporous gold with the pore size of 42 nm.