The invention discloses an NMR nuclear magnetic resonance method for high flux medicine screening. The method includes the following steps: a, preparing mixed water solution containing target biomacromolecules and to-be-screened medicine, and adding the target biomacromolecules and to-be-screened molecules in the water solution and uniformly mixing the biomacromolecules and the to-be-screened molecules as well as the water solution; b, filling the mixed solution in an NMR sample tube, placing the sample tube in a spectrometer, and selectively detecting signals of ligand molecules combined with the target protein, wherein the selective detection includes the steps that firstly, building the selective disturbance for water serving as the resolvent based on the radiation damping effect, secondly, performing the operation based on the effects such as exchange and polarization transfer, and thirdly, exciting the built signals, and selectively detecting the protein and the ligand molecules of the protein, wherein the operation includes two pulse modular units, namely, a signal building module and a detection module; and c, completing the molecule confirmation. The method is simple and convenient to operate and feasible, has high accuracy and sensitivity in experiment detection, and effectively improves the accuracy and efficiency in medicine screening.