Carboxyl-containing metabolites (CCMs) play indispensable roles in cell energy metabolism and cell-cell signaling. Profiling tissue CCMs with spatial signatures is significant for the understanding of molecular histology and may provide new clues to uncover the complex metabolic reprogramming of organisms in response to external or internal stimuli. Here, we develop a sensitive on-tissue CCMs derivatization method, coupled with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), to visualize the spatial distributions of CCMs in biological tissues. A novel reagent, N,N,N-trimethyl-2-(piperazin-1-yl)ethan-1-aminium iodide (TMPA), was synthesized and used for the on-tissue derivatization of CCMs. Meanwhile, the on-tissue derivatization efficiency was significantly improved by introducing acetonitrile gas in the incubation system. With this methodology, a total of 28 CCMs, including 5 tricarboxylic acid cycle intermediates, 20 fatty acids, and 3 bile acids, were successfully detected and imaged in rat kidney tissues. More importantly, the introduction of a quaternary ammonium group into the chemical structure of CCMs enables simultaneous MALDI-MS imaging of tricarboxylic acid cycle intermediates, fatty acids, bile acids, and their metabolic pathway-related metabolites such as carnitines, cholines, glycerophosphocholine, phospholipids, and so on in the positive ion mode. This on-tissue derivatization MALDI-MSI approach was proven to be a powerful tool for probing the distributions and spatial metabolic networks of CMMs in biological tissues.