The invention relates to a method for screening active ingredients of traditional Chinese medicine by nano mesoporous material immobilized target protein. The method includes filling mesoporous material immobilized protein into a chromatographic column, preparing an immobilized target protein inhibitor screening model, dissolving inhibitor having representative inhibiting effect on the immobilized protein into buffer solution to serve as a mobile phase, introducing samples of substrates with saturation concentration every fixed time, collecting peak appearance fraction, replacing the mobile phase with buffer solution free of inhibitor after fixed times, introducing samples of the substrates with saturation concentration every fixed time, respectively freezing and drying the fraction, dissolving the fraction into water, separating the substrates from a product through the analytical type chromatographic column, recording peak area of the product, drawing an inhibition curve of the immobilized target protein inhibitor, checking the model and adopting the prepared model to dissolve aqueous extract of traditional Chinese medicine to be screened into the buffer solution to serve as the mobile phase. Whether the traditional Chinese medicine has inhibition effect or not and the process and the type of the traditional Chinese medicine can be judged according to the peak area of the product. The method has the advantages of high reliability, online performance and the like.