β-type titanium alloys such as a Ti-29Nb-13Ta-4.6Zr alloy (TNTZ) are potential candidates for next-generation metallic biomaterials. However, the mechanical strength of b-type titanium alloys with a single b phase is not enough to be approved as materials for fabricating medical implant devices that are subjected to heavy loads, such as a spinal fixation device. Therefore, β-type titanium alloys are often subjected to aging treatments in order to improve their mechanical strength through precipitation hardening. However, β-type titanium alloys exhibit a heterogeneous microstructure because of microscale elemental segregation. In this study, the heterogeneous microstructure caused by the microsegregation of secondary phases was characterized by field emission scanning electron microscopy (FESEM) in TNTZ subjected to aging treatments. Furthermore, the influence of the heterogeneous distribution of secondary phases in TNTZ on mechanical properties was revealed by comparing its properties to the homogeneously structured TNTZ subjected to long-term homogenization.