Long-term clinical practice shows that Mongolian medicine not only has a unique effect on frequently-occurring and common diseases, but also has particularly remarkable effects on difficult diseases such as cardiovascular diseases, cancer, etc. Molecular imaging technology, which based on imaging technology, displays special molecules on the tissue, cell, and subcellular level. By reflecting the changes on molecular level in vivo, lesions can be located, quantitatively and qualitatively imaged and analyzed. Non-invasive imaging in vivo is the most significant feature of molecular imaging technology. In the research of Mongolian medicine treatment, molecular imaging technology can present the characteristics of the lesions before and after treatment in vivo and in real time, dynamically evaluate the effect of drug treatment, and provide new ideas for exploring the efficacy of Mongolian medicine and developing new drugs.