Natural products originating from plants have various beneficial pharmacological effects, such as anticancer, antimicrobial, and anti-inflammatory activities, while being nontoxic. Therefore, tremendous efforts have been invested in understanding their bioactivities in the body to facilitate therapeutic target validation. However, such research is still challenging for certain natural products, such as flavonoids, which are rapidly metabolized in and eliminated from the human body. To investigate the bioactivities of such products, particularly in certain tissues, it is necessary to understand their biodistribution in vivo. In this respect, reliable analytical methods with simple and efficient procedures for the in vivo evaluation of natural small molecules are urgently required. In particular, mass spectrometry (MS) can be effectively used to analyze small molecules after tissue extraction, as MS has various advantages including accuracy, simplicity, and high sensitivity. Herein, we report the biodistribution of a natural small molecule by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After intravenously injecting gomisin H into a mouse as a model natural product, it was extracted from each organ and then analyzed by MALDI-TOF MS. The analysis showed that gomisin H accumulated mainly in the liver and relatively large amounts of the product existed in the kidney and brain compared to those in other tissues.