Recently, mass spectrometry imaging (MSI) has been drawing more and more attention due to its continuous development and improvement as well as its vital role in the study of biological science. Many MSI-based strategies have been widely applied to the in situ qualitative and quantitative detection and imaging of endogenous/exogenous molecules in tissues. Among, matrix assisted laser desorption/ionization MSI (MALDI-MSI) and desorption electrospray ionization MSI (DESI-MSI) are generally regarded as two the most commonly used molecular imaging techniques. Although MSI, as a histology-based emerging molecular imaging technique, has significant advantages over other imaging techniques because it is a label-free technique which provides high sensitivity, high throughput, and molecular specificity derived from the use of mass spectrometers as detectors for a wide variety of ionized biomolecules in situ within a tissue section, it still has obvious shortcomings in the in situ analysis of low-polarity and neutral biomolecules. To solve this issue, the application of chemical derivatization technology in MSI is one of the most important approaches to overcome these deficiencies of MS molecular imaging. This review provides an overview of various chemical derivatization techniques, such as, esterification derivatization, acylation derivatization, addition reaction derivatization, substitution derivatization, oxidative derivatization, and other derivatizations, used in MS analysis, highlights the application of these chemical derivatization methods in the in situ detection and imaging of biomolecules in tissues by MALDI-MSI and DESI-MSI. It can be predicted that with the advance progress of chemical derivatization technology, the application scope of MSI will be further expanded in the fields of spatial metabolomics, spatial lipidomics, spatial proteomics, and spatial glycomics.