Recently, we selected the antibody fragment with high affinity for the biopolymer film of polyhydroxybutyrate (PHB) from human antibody fragment libraries. In this study, we functionalized CdSe quantum dot (QD) nanoparticles by orderly conjugating the anti-PHB antibody fragments to perform spontaneous and selective stacking of inorganic particles on PHB-coated plates in neutral solutions at room temperature. Surface plasmon resonance analysis showed that the orderly clustering of anti-PHB antibody fragment on QD particles led to no dissociation of QD on PHB-coated plates, indicating the availability of avidity effect. The strong spontaneous immobilization using biomolecular recognition enabled stepwise stacking of inorganic particles on PHB-coated plates only by mixing operation in neutral solutions at room temperature. We show the potential of recombinant anti-material antibody fragments for the bottom-up stacking procedures for hybrid assembly.