Inherited metabolic disorder is a major class of clinical diseases with complexity and difficulty of being diagnosed. Current clinical diagnosis has to rely on the metabolite analysis, gene analysis and enzyme activity (protein function) analysis of these three techniques. We analyse the features of the three diagnostic methods and clinical application of analysis, comparison and induction, to provide some experience and reference that help clinicians to better use of these three techniques. These three ways should be organically combined to form a diagnostic platform for inherited metabolic disorders.