A multispectral integration method to increase the detection limit of gold nanostructures is presented. This method considers all the resonances due to localized surface plasmons, Bloch wave surface plasmons, and Wood’s anomalies. By integrating the wavelength shifts together with intensity changes over these resonances, the detection resolution is increased to about six times larger than that of commonly used wavelength or intensity methods. Further studies with different nanostructures show the detection sensitivity is increased with the decrease of aperture size. The detection limit for 40-nm nanoslits is improved by about seven times relative to that for 300-nm nanoslits. For sub-100-nm apertures, the detection resolution for nanoslits is better than that for nanoholes due to its non-cutoff transmission. The advantage of using the multispectral integration method in biosensing is verified by antigen–antibody interaction experiments.