To propose and establish a mathematical theory of biological systems’ quality grade, which based on the intrinsic laws obeyed by them and fingerprint spectra. Methods: To accurately identify Chinese medicine species based on the systematical theory of Chinese medicines being of identical quality. Then build up quality function depending on the frequency of each peak in fingerprint spectra of a sample set, as the biological systems’ quality information can be represented by stability of peaks in fingerprint spectra of metabolites and secondary metabolites. Then determine different critical frequency scales f≧f-+xSf，x=-0.5, 0, 0.5, 1. The quality of fingerprint peaks in a sample set varies distinctively because of different critical frequency scales. Next, to decide fingerprint peaks and their number of different quality grade fingerprint peaks in the sample set, and that of each sample from excellent rank to qualified rank respectively. As a result, the quality grade of each sample can be ascertained relying on the theoretical standard. The ratio of its peak number to the total peak number belongs to a certain grade, which is equal to or lager than 61% and is obtained from the biological heredity and variation evolution information theory-the dual index information theory. The distinguish procedure should be order from excellent rank to qualified rank. Results: The approach was confirmed by analyzing the infrared fingerprint spectra of components, which are extracted from 22 Shiquan Dabu pills and 9 Buzhong Yiqi pills from different corporations with chloroform. The quality grades of 22 Shiquan Dabu Pills were detected. The results indicated that these samples all belong to excellent rank though there are some differences among their characteristic sequences. Conclusion: This mathematical theory to determine biological system quality grade might be a good approach for any kind of biological systems, theoretically or quantitatively speaking. Besides, the peaks ranking at excellent grade might be as the characteristic marker group of the biological species.