A series of ultrathin, homogenous gold nanoparticle (AuNP) substrates for surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) were prepared using a simple air/water interface approach. These SALDI substrates enabled soft ionization and provided significant improvements in terms of signal intensities and reduced background levels in comparison to other AuNP morphologies for different analytes such as fatty acids, peptides, amino acids, saccharides, and drugs. Through different microscopic and spectroscopic methods, we determined that the packing homogeneity of the [AuNP]n substrates played a vital role in the efficiency of the SALDI process. We demonstrated that the signal intensities of the investigated analytes were readily optimized by manipulating the thickness of the [AuNP]n substrates. The desorption/ionization efficiency increased as a function of the number of layers and then reached a saturation point. The optimized [AuNP]n substrates not only exhibited high SALDI-MS desorption/ionization efficiencies but also showed excellent reproducibilities of the analyte signals.