The invention relates to a preparation method of a thixotropic agent for a cement-based system and belongs to the technical field of thixotropic agent preparation. The preparation method includes enabling corn starch to react with epoxy chloropropane under the alkaline condition prior to gelatinization, enabling the gelatinized corn starch and acrylonitrile to polymerize under the action of an initiator so as to obtain a polymer of a network structure, enabling coconut oil to react with ethylene glycol butyl ether under the alkaline condition when flow loss is small under the action of shear force so as to obtain a fatty acid salt, compounding the fatty acid salt with the polymer to obtain a thixotropic agent base solution, and mixing the thixotropic agent base solution with sodium dodecyl benzene sulfonate and hydroxyethyl cellulose. The thixotropic agent for the cement-based system, prepared by the preparation method, is excellent in thixotropic performance at high temperatures and is 70-75 mL in water loss after being stirred for 30 minutes at the temperature of 75 DEG C, and compressive strength of cement mortar is improved and can reach 22-25 MPa after 24-hour curing.