Herein, we successfully synthesized a magnetic mesoporous material, Fe3O4@SiO2@mSiO2, and acetylcholinesterase (AChE) was immobilized by a covalent bonding method. The tolerance ability of immobilized AChE (by magnetic mesoporous silica nanoparticles) in different organic solvents was better than that of free AChE. Furthermore, the magnetic character of the fixed AChE improved the detection sensitivity and reliability for carbofuran, methomyl, isoprocarb, and carbaryl. The limit of detection (LOD) of carbofuran, methomyl, isoprocarb, and carbaryl was 0.01, 0.22, 0.26, and 0.43 μM, respectively. It shows a good correlation between carbamate pesticides (CMs) and the inhibition rate of Fe3O4@SiO2@mSiO2-AChE in a given concentration range. The linear ranges of carbofuran, methomyl, isoprocarb, and carbaryl were 0.02–0.90, 0.31–12.33, 0.27–5.17, and 0.50–14.91 μM, respectively. Chinese cabbage and cucumber spiked with four CMs were used as field-incurred samples to prove the feasibility of the developed method. According to the maximum residue limits, the results were satisfactory, with recovery rates between 77.03 and 110.07%, and the RSDs ranged from 3.17 to 6.79%. The stability of immobilized AChE in organic solvents was improved with enhanced sensitivity for detecting pesticide residues.