Perfluorooctanesulfonic acid (PFOS) is an emerging environmental organic pollutant that has been widely used in daily life products in the last century. Numerous studies showed that the accumulation of PFOS in human through food chain would lead to various disease. However, there is currently no report about its in situ localization in the tissue. In present study, we aimed to develop a reproductive and less-cost method to quantitatively detect and determine the spatial distribution of PFOS in mouse kidney by matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) with a commercially available matrix. α-Cyano-4-hydroxycinnamic acid (CHCA) matrix was optimized for PFOS detection in MALDI-IMS analysis. Compared to other organic matrices, CHCA used in negative ion mode showed less background interference and enhanced MS signal intensity and high spatial resolution (80 μm) for PFOS analysis. The use of a CHCA matrix with an autospray system led to successful identification of the PFOS ion signals on the perfusion kidney tissue. The detection limit was at the μg/mL level, with direct visualization from a MS image. The developed method with the optimized parameters was successfully employed to obtain the PFOS spatial distribution in the kidney collected from mice after the PFOS exposure for 14 days. PFOS was mainly distributed in the kidney cortex region, which was consistent with the histological analysis results. Taken together, a rapid, economic, and efficient method was developed for PFOS detection by MALDI-IMS using a CHCA matrix. Mapping the distribution of PFOS by MALDI-IMS with a CHCA matrix provides an innovative approach for the analysis of environmental pollutants in animal or human tissues.