The applications of organic matrices for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) are reviewed. Recent advances of MALDI-MS using organic matrices, including the applications of ionic liquids matrices (ILMs) and organic matrices modified/conjugated nanoparticles, are covered. Organic matrices are applied for many other applications such as derivatization or capping agents of nanoparticles, eluent for chromatography, internal standard for quantitative analysis and as reagents for the synthesis of eco-friendly solvents (ILMs). Within the field of nanotechnology, organic matrices@nanoparticles have a dominant position, and the last decade has seen remarkable growth for these hybrid materials. Selection of the optimum organic matrices is paramount important and critical for the analysis using MALDI-MS. Factors such as additives, instrument set up and sample preparation affect greatly the results of analysis. Advanced techniques using organic matrices are also highlighted.