This invention provides molecularly imprinted polymer nanoparticles compatible with biological samples, and in particular pure biological samples and a preparation method thereof. Said molecularly imprinted polymer nanoparticles have a crosslinking degree exceeding 50%, a particle diameter of 10 to 500 nm, hydrophilic polymer brushes on its surfaces and can be prepared by introducing appropriate hydrophilic macromolecular chain transfer agents into reversible addition-fragmentation chain transfer (RAFT) precipitation polymerization systems through the one-pot synthesis. The preparation method is simple, features a broad range of application and yields a pure product. The obtained hydrophilic molecularly imprinted polymer nanoparticles have prospects for a wide range of application in biological sample analysis, medical clinical immune analysis, food and environmental monitoring, biomimetic sensors, etc.