The invention provides a crystal modifier, medical flaky alpha-hemihydrate calcium sulfate and a preparation method thereof. The preparation method of the medical flaky alpha-hemihydrate calcium sulfate comprises the following steps: step 1, respectively preparing a calcium salt solution and a sulfate solution, mixing the calcium salt solution and the sulfate solution according to the molar mass ratio of calcium salt to sulfate of 2.5-4:1, adding a trihydroxymethyl propane tris (3-mercaptopropionic acid ester) maleic acid crystal modifier, uniformly stirring, and adjusting pH to 5.5-6.5 to obtain white slurry; step 2, fully stirring and refluxing the prepared slurry in a reactor at 90-100 DEG C to obtain alpha-hemihydrate calcium sulfate slurry; and step 3, performing suction filtering, washing and drying on the slurry. The method can prepare flaky alpha-calcium sulfate hemihydrate crystals with high purity, small particle size and uniform distribution, which meet the requirements of medical implant bone repair materials. The diameter of the flaky alpha-calcium sulfate hemihydrate crystals is less than 5 mu m, the aspect ratio is less than 0.5, the maximum bending strength is as high as 21.4 MPa, and the compressive strength is as high as 50.7 MPa.