Precisely controlling the protein-nanomaterial interactions at selective sites is crucial in engineering biomolecule composite architectures with tailored nanostructures and functions for a variety of biomedical applications. This strategy, however, is only beginning to be explored. Here, we demonstrate the facet-specific assembly of proteins, such as albumin, immunoglobulin and protamine, on {100} facets of SrTiO3 polyhedral nanocrystals, while none on {110} facets. Molecular dynamics simulations indicate the immobile surface hydration layer might play a barrier role to effectively prevent proteins adsorption on specific {110} facets. This work thus provides new insights into the fundamentally understanding of protein-nanomaterial interactions, and open a novel, general and facile route to control the selective adsorption of various proteins on various nanocrystals.