Monoclonal antibodies and antibody-derived biologics are essential tools for cancer research and therapy. The development of monoclonal antibody treatments for successful tumor-targeted therapies took several decades. A nanobody constructed by molecular engineering of heavy-chain-only antibody, which is unique in camel or alpaca, is a burgeoning tools of diagnostic and therapeutic in clinic. In this study, we immunized a 4-year-old female alpaca with TIM-3 antigen. Then, a VHH phage was synthesized from the transcriptome of its B cells by nested PCR as an intermediate library; the library selection for Tim-3 antigen is carried out in three rounds of translation. The most reactive colonies were selected by periplasmic extract monoclonal ELISA. The nanobody was immobilized by metal affinity chromatography (IMAC) purification with the use of a Ni-NTA column, SDS-PAGE, and Western blotting. Finally, the affinity of TIM3-specific nanobody was determined by ELISA. As results, specific 15 kD bands representing nanomaterials were observed on the gel and confirmed by Western blotting. The nanobody showed obvious specific immune response to Tim-3 and had high binding affinity. We have successfully prepared a functional anti-human Tim-3 nanobody with high affinity in vitro.