In this study, the novel magnetic molecularly imprinted polymers were successfully synthesized by surface imprinting technique and used as magnetic adsorbent for extracting six strobilurin fungicides from agricultural products. The magnetic molecularly imprinted polymers showed the typical core-shell structure with high maximum adsorption capacity (42.7 mg/g) and rapid adsorption equilibration (3 min) and specific recognition ability. The parameters (elution solvent, elution time, adsorption time, loading solvent and solution pH) in magnetic solid phase extraction were evaluated. Under the optimum adsorption and desorption condition, the magnetic solid phase extraction process based on magnetic molecularly imprinted polymers coupled with high performance liquid chromatography-tandem mass spectrometry was developed for the sensitive detection of strobilurin fungicides from agricultural products. The developed method presented good linearity (5–200 ng/mL) with correlation coefficients (R2) ≥ 0.9990. The limits of detection and quantification were 0.03–0.49 ng/g and 0.09–1.64 ng/g, respectively. At the three different concentration (20, 50, 100 ng/g) spiked in agricultural products, the good recovery (71.5%−115.8%) was obtained and the relative standard deviations were below 8.3%. These results indicated that this established method was sensitive, accurate, selective and reproducible.