This study developed an open-source method, x-dimensional mass spectrometry imaging (MSI(x)), to reveal the spatially-resolved high-order metabolomics information associated with disease progression or drug action. This high order bioinformation includes metabolism pathway, species, biofunction, or biotransformation, which involves multiplex metabolites and cannot be presented by a single ion image. The MSI(x) enables the evaluation of the physiological status, the discovery of therapeutic or adverse effects, the investigation of regional heterogeneous response to drug treatment, possible molecular mechanism, and even drug potential target. MSI(x) was demonstrated to be a promising molecular imaging tool not only for efficacy and safety evaluation but also for the molecular mechanism investigation at the early stage of drug research and development.