Malachite green (MG) is currently posing a carcinogenic threat to the safety of human lives; therefore, it is highly desirable to develop an effective method for fast trace detection of MG. Herein, for the first time, this paper presents a systematic study on polymer microspheres, being prepared by combined Pickering emulsion polymerization and molecular imprinting, to detect and purify MG. The microspheres, molecularly imprinted with MG, show enhanced adsorption selectivity to MG, despite a somewhat lowered adsorption capacity, as compared to the counterpart without molecular imprinting. Structural features and adsorption performance of these microspheres are elucidated by different characterizations and kinetic and thermodynamic analyses. The surface of the molecularly imprinted polymer microspheres (M-PMs) exhibits regular pores of uniform pore size distribution, endowing M-PMs with impressive adsorption selectivity to MG. In contrast, the microspheres without molecular imprinting show a larger average particle diameter and an uneven porous surface (with roughness and a large pore size), causing a lower adsorption selectivity to MG despite a higher adsorption capacity. Various adsorption conditions are investigated, such as pH and initial concentration of the solution with MG, for optimizing the adsorption performance of M-PMs in selectively tackling MG. The adsorption kinetics and thermodynamics are deeply discussed and analyzed, so as to provide a full picture of the adsorption behaviors of the polymer microspheres with and without the molecular imprinting. Significantly, M-PMs show promising solid-phase extraction column applications for recovering MG in a continuous extraction manner.