Abstract: Mass spectrometry imaging (MSI) is a label-free molecular imaging technique whereby to simultaneously measure and map multiple biomolecules directly from tissue sections. It is reported that MSI analysis of metabolites has undergone a fast development and has been developed into a powerful tool for drug development and discovery in recent years. However, some problems, such as molecule covering range, sensitivity of metabolite detection, and the interference from the complicated biological matrix are still remaining as challenges for current MSI technologies. To tackle with these problems, our group previously developed an air flow assisted ionization (AFAI) MSI platform, and successfully applied it on in vivo pharmaceutical analysis. Aiming at increasing the sensitivity and specificity of in vivo pharmaceutical analysis, an integrated MSI method to simultaneously image drug and endogenous metabolites in whole body tissue section was developed using AFAI-MSI in a full mass scan mode. This method can acquire not only the distribution of drugs and its metabolites, but also enormous various endogenous metabolites in one experiment, as resulted to obtain in situ spatial and chemical information of parent drugs and metabolites in whole-body tissue sections; and the target organs of drugs can be directly mapped. Based on our previously reported AFAI ion source, we modified the interface to couple the AFAI ion source on a Q-orbitrap mass spectrometer, and constructed an new AFAI-MSI device, and further specifically programed the data features (high resolution MS data) into our MSI software, finally achieved rapid and reliable MSI analysis of tissue section, along with high stability and accuracy information for metabolite identification. The drug candidate S-(+)-deoxytylophorinidine (CAT) was selected to study the spatial distribution in rat. AFAI-MSI analysis was performed for the administered tissue sections along with the data acquiring in high mass resolution full scan mode and targeted selected ion scan mode, and the distribution and dispersion of CAT in rat euthanized at different time points (30 min and 2 h) were acquired accurately and specially. By integrating the advantage of air flow-assisted ionization (AFAI) and high resolution mass spectrometry imaging (HRMSI), a high specified MSI method has been developed to improve accuracy and reliability for the simultaneous mapping drug and endogenous metabolites in whole-body rat tissue section. The acquired information of the endogenous metabolites lay a foundation to disclose the relevance of the biological transformation pattern and distribution characteristic with the effect and toxicity of new drugs, thus providing critical basis for the early prediction of drug effect and toxicity. The study demonstrated that the simultaneous imaging drug and the endogenous metabolites can be realized by high mass resolution AFAI-MSI analysis in a single experiment, which will provide an alternative way for the earlier drug discovery.