Microdialysis (MD) is a biochemical micro-detection technique that can continuously sample and analyze the endogenous or exogenous substances in the intercellular fluid, with no impact on the internal environment of the organism. MD can be used to determine not only the local drug pharmacokinetics in internal organs or tumors but also the pathophysiological processes that have metabolic products or organ specificity, and even may be used as an approach for direct delivery and assessment of the local drug in organs and tumors. In this paper, the authors address the application of MD in dealing with pancreas-related research, and discuss its advantages and limitations, as well as the future prospects.