Sample preparation such as isolation and pre-concentration is a crucial step for the phytochemical analysis. Magnetic solid-phase extraction (MSPE) has received considerable attention, mainly due to its phase separation more conveniently by facile magnetic decantation as compared to traditional SPE. This review focused on the recent applications of MSPE in sample preparation for the analysis of phytochemical compounds in plants, biological samples and Chinese herbal preparations. In addition, the enzymes immobilized on the magnetic materials and used for the biospecific extraction of enzyme inhibitors were also discussed. The information summarized in this article may provide a reference to the further applications of MSPE in phytochemical analysis.