The invention discloses a preparation method for a high-performance low-modulus medical titanium alloy three-dimensional metal part, and belongs to the technical field of electron beam machining. The preparation method is suitable for rapid-forming preparation of a low-modulus medical titanium-alloy-system complex-structure metal part containing 10-35 wt% of Ti-Nb, 0-15 wt% of Zr, and 0-15% of Sn and Ta. The preparation method comprises the steps that firstly, the titanium alloy three-dimensional metal part is prepared through the EBM technique; secondly, hot isostatic pressing treatment is conducted on the prepared three-dimensional part at the temperature of 900-1200 DEG C; and finally, heat treatment is conducted on the titanium alloy part. Through the technological process, the excellent-comprehensive-mechanical-performance low-modulus medical titanium alloy complex-structure three-dimensional part with the compressive strength being 5 MPa or over, the tensile strength being 600 MPa or over, the elasticity modulus being lower than 90 GPa, the ductility being 10% or over and the fatigue strength being 300 MPa or over can be obtained, and the preparation method can be widely applied to the medical field and the like.