Chromatin-associated proteins are essential for maintaining chromatin structure, regulating gene expression, and epigenetic regulation. However, isolating nuclear proteins from plants with high purity is very difficult due to significant background contamination from cytoplasmic proteins, organelle proteins, and metabolites. In the present study, we build a method for isolating chromatin-associated proteins. This method does not need to isolating nuclei, and can directlty purify DNA-protein (DNP) complex.