Proteins, which have complex structures and fall under diverse categories, are closely associated with different kinds of life activities. Majority of the proteins exist in low concentrations in complex biological samples, because of which their direct analysis without sample pretreatment is difficult. Thus, selective separation of the target proteins from complex biological samples is essential for efficient analysis. Molecularly imprinted polymers, containing numerous imprinted cavities that are complementary with the templates in terms of shape, size, and functional groups, have great potential for use in the selective recognition and separation of the target proteins from complex biological samples. However, the large size, structural flexibility, and complex structures of proteins hinder their efficient separation and analysis by conventional molecular imprinting technology. In this review, several novel molecular imprinting techniques, including surface imprinting, epitope imprinting, and metal chelate imprinting, are introduced. The emergence of these novel technologies has contributed to advances in protein analysis. The applications of these molecular imprinting techniques to the separation and analysis of proteins in the last three years are summarized herein. Finally, the promising future of molecular imprinting techniques in the area of proteins is prospected.