Although some important biomarkers for myocardial injury have been identified, there still lacks a systematic view of the development and progression of myocardial infarction, including enzymatic regulation, metabolite levels, fluxes, etc., which are pivotal to elucidate the physiological mechanism of disease. Here we present an untargeted analytical approach based on gas chromatography coupled with mass spectrometry (GC-MS) to map the temporal metabolic profilings in blood sera of myocardial infarction rat model prepared by left coronary artery ligation. Using XCMS software (http://metlin.scripps.edu/download/), data processing was simplified greatly. We identified the changes in circulating levels of 24 metabolites during the myocardial ischemia. By combination of previous proteomic results, it gives rise to a new insight view of energy metabolism changes referring to anaerobic glycolysis, citric acid cycle, fatty acid beta-oxidation, and some amino acids metabolism. With these altered metabolism pathways as possible drug targets, we validated a role for the presented metabonomic profiling in the systematic understanding of the action mechanism of component-complex medicine herbs, such as Radix Ophiopogonis, a widely-used anti-myocardial ischemia herbal medicine in Asia.