The noxious clenbuterol misapplied as the feed additive has posed an enormous threat to humans who actively rely on the food chains with high potential of contamination by clenbuterol, such as pork and beef. It is, therefore, highly desirable to develop novel materials and strategies for dealing with the clenbuterol. Herein, functional polymer microspheres prepared by Pickering emulsion polymerization were explored for the selective enrichment of the clenbuterol, and their structure and oxygen functionalities could be tailor-made by a molecular imprinting process. The clenbuterol imprinting was adequately demonstrated to not only increase the particle size (~52 nm vs. ~42 nm) and create cavities for the accommodation of the clenbuterol molecules, but also reduce the oxygen functionalities of the resulting molecularly imprinted polymer microspheres (MIPMs) by approximately 4 at.%, which is believed to correlate with the high specificity of the MIPMs. Various characterization methods were employed to evidence these findings, including scanning electron microscopy, BET measurements, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and elemental mapping examination. More importantly, the MIPMs showed a markedly superior enrichment capability towards clenbuterol to the counterpart, that is, non-molecularly imprinted polymer microspheres (NIPMs). Compared to the NIPMs without specificity for clenbuterol, the MIPMs exhibited an impressive selectivity to clenbuterol, with the relative selectivity coefficient (k′) values largely exceeding 1, thus corroborating that the useful molecular imprinting led to the generation of the binding sites complementary to the clenbuterol molecule in the size and functionalities. The MIPMs were also employed as the stationary phase to fabricate molecularly imprinting solid-phase extraction column, and the spike recovery was demonstrated to be not significantly decreased even after nine cycles. Furthermore, the reliability of the method was also evidenced through the comparison of the MIPMs prepared from different batches.