Surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) is a valuable technique for detecting small molecules in environmental and medicinal studies. We investigated dot-like and 2D-array gold nanoparticle-based SALDI-MS substrates that excite surface plasmons and enhance the desorption/ionization of sample molecules via charge transfer between the substrate and sample molecules. We aimed to optimize the nondissociative detection of sample molecules by efficiently transferring energy while suppressing excess internal energy. SALDI-MS measurements using crystal violet (CV) molecules revealed ion intensity and spectral pattern differences between the dot-like and 2D-array substrates. SALDI-MS measurements using dot-like substrates suggested two desorption/ionization processes: internal energy supply and charge transfer between the substrate and sample molecules. However, SALDI-MS measurements using 2D-array substrates suggested that the internal energy supply was suppressed. As a result, the dot-like substrate provided higher desorption/ionization efficiency but increased fragmentation, whereas the 2D-array substrate was suitable for highly sensitive and nondissociative SALDI-MS measurements. This study contributes to the optimization of SALDI-MS measurements and advances our understanding of energy transfer and sample molecule dissociation.