This application relates to molecular biology, and more specifically to a method which uses the molecular recognition between a target molecule ligand and an aptamer, magnetic separation and MS qualitative and quantitative analysis to enable the association between the detection of multi molecules and information of multiple functional groups, and effectively determine the correlation between molecules and functional groups of the body or tissue. This application can easily purify the target molecules by magnetic separation and can effectively obtain the target molecule group based on the high specificity and affinity of the aptamer. In addition, based on the MS detection, this application can effectively perform the qualification and quantification of the multi molecules, achieving the secondary molecular detection and improving the detection accuracy. The simultaneous qualification and quantification of multi molecules can not only accurately reflect the relationship among molecules, but also reveal the interrelationship among body functions, playing a significant role in the proteomics and genomics research and clinical molecular detection.