Inherited metabolic disorders (IMD), also known as inborn errors of metabolism, is a rare disease in terms of incidence rate. The incidence of single disease is relatively low. However, the prevalence rate is higher as a group of diseases. So far, more than 700 kinds of IMD diseases have been found with the gradually increase improvement of molecular diagnosis technology. There are many difficulties and challenges in the accurate diagnosis of IMD due to the variety of IMD involved genes, the complexity of clinical symptoms and the lack of specificity. In this paper, the molecular basis, the idea to diagnosis, the detection methods and problems in clinical application with IMD will be discussed.