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The purpose of this study was to synthesize a magnetic material that could be easily separated by a magnetic field and combined the catalytic function of an acid/base ionic liquid with silicon for biodiesel preparation. A kind of magnetic catalyst-immobilized ionic liquid was synthesized by a three-step method. The synthesis conditions in each step were optimized by single-factor analysis. Under the optimum conditions, 206.83 mg of ionic liquid (>43.63%) was immobilized on SiO2 (per gram). Heating under reflux was applied to extract Schisandra chinensis seed oil with an average yield of 10.9%. According to the biodiesel yields, Fe3O4@SiO2@[C4mim]HSO4 was the most efficient catalyst in the methyl esterification reaction. Under the optimum reaction conditions, seed oil (10.0 g) was mixed with methanol (70 mL) under continuous mechanical stirring for 3 h, and the yield of biodiesel was 0.557 g/g (the catalyst efficiency was about 89.2%). Also, the thermal value was increased from 32.14 kJ/g (seed oil) to 38.28 kJ/g (biodiesel). The catalytic efficiency of Fe3O4@SiO2@[C4mim]HSO4 was 87.6% of the first being used after four reuse cycles, and 71.4% of the first being used after six reuse cycles in the methylation reaction. The yields and physical and chemical properties of biodiesel were determined.