Titanium-based implants are often utilized in oral implantology and craniofacial reconstructions. However, the biological inertness of machined titanium commonly results in unsatisfactory osseointegration. To improve the osseointegration properties, we modified the titanium implants with nanotubular/superhydrophilic surfaces through anodic oxidation and thermal hydrogenation and evaluated the effects of the machined surfaces (M), nanotubular surfaces (Nano), and hydrogenated nanotubes (H-Nano) on osteogenesis and osseointegration in vitro and in vivo. After incubation of mouse bone marrow mesenchymal stem cells on the samples, we observed improved cell adhesion, alkaline phosphatase activity, osteogenesis-related gene expression, and extracellular matrix mineralization in the H-Nano group compared to the other groups. Subsequent in vivo studies indicated that H-Nano implants promoted rapid new bone regeneration and osseointegration at 4 weeks, which may be attributed to the active osteoblasts adhering to the nanotubular/superhydrophilic surfaces. Additionally, the Nano group displayed enhanced osteogenesis in vitro and in vivo at later stages, especially at 8 weeks. Therefore, we report that hydrogenated superhydrophilic nanotubes can significantly accelerate osteogenesis and osseointegration at an early stage, revealing the considerable potential of this implant modification for clinical applications.