The invention relates to a micromolecule mu-PA inhibitor (3R,12aS)-3-(4-aminobutyl)-2,3,6,7,12,12a-hexahydropyrazino[1',2':1,6]pyrido[3,4-b]indole-1,4-dione with the structural formula shown in the specification, relates to a preparation method of the compound and application of the compound to inhibit tumor invasion and migration, resist coagulation and diminish inflammation as the mu-PA inhibitor. The invention belongs to the field of biological medicine.