Beta-type Ti-29Nb-13Ta-4.6Zr (TNTZ) was recently developed as a representative biomedical Ti alloy. As-solutionized TNTZ has a low Young's modulus less than 60 GPa close to that of cortical bone along with very low cytotoxicity and good bone biocompatibility. Solution treatment and aging (STA) is a typical heat treatment for improving the mechanical properties of beta-type titanium alloys. However, STA also drastically increases the Young's modulus. Therefore, this study investigated the effects of surface modification, micro-shot peening, on the mechanical properties of TNTZ subjected to severe thermomechanical treatment in order to maintain a relatively low Young's modulus. The bone contact characteristics of TNTZ samples subjected to surface modification and cancellous bone were also compared. The Vickers hardness of cold-swaged TNTZ (TNTZSW) subjected to micro-shot peening was significantly increased within 20 μm from the very edge of the specimen surface. The fatigue strength of TNTZSW subjected to micro-shot peening increased especially in the high cycle fatigue life region. The fatigue limit was around 400 MPa. The bone formations on TNTZSW subjected to micro-shot peening and TNTZSW with the mirror surface as comparison material were almost identical to each other. However, the relative bone contact ratio of TNTZSW subjected to micro-shot peening was better than that of TNTZSW with the mirror surface.