We have demonstrated that cysteine and glutathione induced edge-to-edge coupling of gold nanocubes (Au NCs) caused a band-selective enhancement of two-photon photoluminescence (TPPL). The photoluminescence intensity of the X-band of Au NCs was found to be enhanced up to 60-fold and 46-fold upon addition of cysteine and glutathione, respectively, while the intensity of L-band remained almost unchanged. This band-selective enhancement behavior is totally different from the previously observed aggregation enhanced TPPL of spherical metal nanoparticles (NPs). The band-selective enhancement was ascribed to preferential enhancement of the X-band emission through resonant coupling with longitudinal surface plasmon resonance (SPR) band of the Au NCs assembly. This phenomenon was utilized to develop a new two-photon fluorescence turn-on sensing platform for detection of cysteine and glutathione. This method displayed high sensitivity and excellent selectivity over the other 19 amino acids. Together with the advantage of deep tissue penetration and localized excitation of two-photon near-infrared excitation, this strategy has promising applications in in vivo biosensing and imaging.