Great endeavors are undertaken to find effective nanoparticles to replace organic matrices for the analysis of small molecules using laser desorption ionization mass spectrometry (LDI-MS). Nanoparticles offer high sensitivity and better selectivity compared to conventional organic matrices. Surface assisted LDI-MS (SALDI-MS), and surface enhanced LDI-MS (SELDI-MS) provide clear background spectra without observable interferences peaks, and cause no fragmentation (soft ionization) of thermal and acidity labile molecules. This review article (with 460 references) summarizes the recent applications of nanoparticles including metallic, metal oxides, silicon, quantum dots, metal-organic frameworks and covalent organic frameworks, for the analysis of small molecules. Nanoparticles serve not only as surface for LDI-MS, but they can be also used as probe or pseudo-stationary phase for separation, enrichment, and microextraction. Hopefully, the knowledge and learning points gained from this review will deepen the understanding of nanoparticles applications for LDI-MS.