During the last few years, separation techniques using molecularly imprinted polymers (MIPs) have been developed, making breakthroughs using magnetic properties. Compared to conventional MIPs, magnetic molecularly imprinted polymers (MMIPs) have advantages in sample pretreatment due to their high specificity and selectivity towards analytes as a result of their larger specific surface areas and highly accessible specific binding sites. The techniques of isolation of active compounds from natural products usually require very long process times and low compound yields. When MMIPs are used in sample separation as Solid Phase Extraction (SPE) sorbents, the MMIPs are introduced into the dissolved sample and spread evenly, and they form bonds between the analyte and the MMIPs, which are then separated from the sample matrix using an external magnetic field. This process of separating analytes from the sample matrix makes the separation technique with MMIPs very simple and easy. This review discusses how to synthesize MMIPs, which factors must be considered in their synthesis, and their application in the separation of active compounds from natural products. MMIPs with magnetic core-shells made by co-precipitation can be a good choice for further development due to the high synthesis yield. Further optimization of the factors affecting the size and distribution of magnetic core-shell particles can obtain higher synthesis yields of MMIPs with higher adsorption capacity and selectivity. Thus, they can isolate target compounds from natural plants in high yields and purity.