The invention relates to the technical field of screening of natural medicines and provides a high-content rapid screening method for magnetic beads of ocean natural active materials. The method is a screening and evaluating method for active materials based on magnetic bead bonds and high-content multi-target protein integration. According to the high-content rapid screening method, the configuration is as follows: a hardware system is composed of a permanent magnet, the magnetic beads and targets; a software system is responsible for acquiring hygroplasm data. Compared with a conventional ultraviolet screening method, the screening method has the advantages that the screening efficiency is obviously improved and the screening time is shortened; various biological activities can be investigated at the same time and the synergistic effect among compounds is found. The screening method is rapid, accurate, great in information amount and good in repeatability and can be used for screening a natural product library or a combinatorial chemistry library in a large scale.