The invention relates to a shale inhibitor for a drilling fluid based on a microemulsion ionic liquid and a preparation method thereof. The shale inhibitor is prepared from the following components inpercent by mass: 35-45% of an ionic liquid, 10-15% of normal butanol, 3-6% of potassium chloride, 2-5% of nano calcium carbonate, 3-5% of polyoxyethylene sorbitan fatty acid ester, 1-3% of sorbitan aliphatic ester and the balance of water. By adopting an ionic liquid microemulsion synthesizing method, the shale inhibitor can exist in microemulsion cores stably. The coordinate repression of a system is further enhanced by adding KCl. The stability of the microemulsion in the drilling fluid is enhanced by using nano calcium carbonate. The nano calcium carbonate exists in form of double continuous microemulsion liquid drops in the drilling fluid, so that the shale inhibitor has certain slow release action after the drilling fluid to play a long-acting role. The relative expansion reduction rate of clay of the shale inhibitor for the drilling fluid based on the microemulsion ionic liquid exceeds 85%, and the triple shale rolling recovery rate exceeds 95%.