Novel core–shell magnetic molecularly imprinted polymers (MMIPs) were synthesized using the sol–gel method for the adsorption of cefixime (CFX). Fe3O4@SiO2 is the core, and molecularly imprinted polymers (MIPs) are the shell, which can selectively interact with CFX. The preparation conditions, adsorption kinetics, adsorption isotherms, selective adsorption ability, and reutilization performance of the MMIPs were investigated. The adsorption capacity of MMIPs for CFX was 111.38 mg/g, which was about 3.5 times that of MNIPs. The adsorption equilibrium time was 180 min. The dynamic adsorption experiments showed that the adsorption process of MMIPs to CFX conformed to the pseudo-second-order model. Through static adsorption study, the Scatchard analysis showed that MMIPs had two types of binding sites—the high-affinity binding sites and the low-affinity binding sites—while the Langmuir model fit the adsorption isotherms well (R2 = 0.9962). Cefepime and ceftiofur were selected as the structural analogs of CFX for selective adsorption studies; the adsorption of CFX by MMIPs was higher than that of other structural analogs; and the imprinting factors of CFX, cefepime, and ceftiofur were 3.5, 1.7, and 1.4, respectively. Furthermore, the MMIPs also showed excellent reusable performance.