In order to assess the contribution of adenosine triphosphate and its metabolites to the cellular metabolism process in Saccharomyces cerevisiae, it is very important to simultaneously determine the relative concentrations of ATP and its metabolites. In this study, a fast, simple reversed-phase high-performance liquid chromatography with high selectivity was developed to simultaneously measure adenosine triphosphate and its metabolites (adenosine diphosphate, adenosine monophosphate, and cyclic adenosine monophosphate) in yeast. The method was performed under the gradient grogram, and the detection was monitored at 254 nm. Analysis was achieved within 25 min. The four components can be detected with linear response over the concentration range from 1 to 100 mg L−1 with excellent correlation coefficients (r2) > 0.999. The recovery of the four analytes was 92.9%, 90.4%, 99.1%, and 105.1%, respectively. To demonstrate the good analysis of yeast samples, changes in the four adenine nucleotides levels caused by caloric restriction in yeast were determined. It is expected that the current method may contribute to further metabolomics and system biology investigations of yeast.