Chirality is a widespread phenomenon in nature, which plays an essential role in the metabolism of organisms. It is highly associated with a lot of significant biological processes, such as transport and translocation of proteins. Herein, we reported a chiral anodic aluminum oxide (AAO) nanochannel modified with both titanium dioxide (TiO2) nanostructures and cysteine (Cys) enantiomers and explored the chirality response on bovine serum albumin (BSA) transport. The results showed that BSA was preferentially transported through the nanochannel modified with l-Cys due to chiral interaction, which indicated that chirality would influence the transport process of proteins strongly. TiO2 nanostructures, which were anchored on the wall of a nanochannel, improved the sensitivity of the selective transport process of BSA. Moreover, we found that the effect of TiO2 nanostructure modification was more stable and excellent when the pore diameter of AAO membrane was 40–70 nm. This study provided a platform for the research of chiral selective transport of proteins, and introduced metal oxide nanostructures into a biomimetic nanochannel as well.