The invention belongs to the field of modern isolation analysis materials science and engineering, it relates to preparation method and application of microwave assistant molecular print magnetic microsphere, the procedure as follows: adopting microwave chemical reactor, taking nanometer magnetic fluid as magnetic nuclei, by cleaning and external modification, ultrasound detracting to water; mounted pattern molecule and functional monomer self-assembly; adding polymeric liquor by step, cross link agent and initiator, making it mixes and separates with magnetic fluid fully by stirring of machine, microwave procedure controlled temperature and heats up, until raising polymerization; Magnetic separates the foregoing magnetic microsphere, removing mounted pattern molecule, vacuum drying, aging. The molecular print magnetic microsphere has not only recognize ability of mounted pattern molecule and its analogue, but also has the approved characteristic of 'gathering hyphen recycle', the process of preparation heats up with microwave, decreasing the time of print aggregation, improving homogeneity and print efficiency of polymer form. The molecular print magnetic sphere applies to gather, isolate and analysis of structure analogue in the environmental sample, eatable etc complex samples.