This invention discloses a method for preparing BaTeMo2O9 crystal and its application. The crystal belongs to monoclinic system, and the space group is P21. The method comprises: adding BaTeMo2O9 polycrystalline powder into appropriate fluxing agent system (TeO2-MoO3, MoO3, TeO2, B2O3 or PbO-B2O3), placing in a Pt crucible, heating to melt the raw materials, mixing adequately, cooling to the melt saturation point, adding seed crystals, and growing homogeneous nonlinear optical BaTeMo2O9 single crystal with lengths exceeding 10 mm and thickness exceeding 5 mm. The obtained BaTeMo2O9 single crystal has strong frequency multiplification effect and IR absorption edge greater than 5000 nm, and has such advantages as high stability, no decomposition at room temperature, and no deliquescence. The crystal has nonlinear optical, electro-optical and piezoelectric applications. The method has such advantages as easy operation,and abundant raw materials.