The present invention relates to a bio-silica chip comprising a silica-binding protein and a fabrication method thereof, and more particularly to a bio-silica chip in which a fusion protein of a silica-binding protein and a probe protein is immobilized on a chip comprising a silica layer, a fabrication method thereof and a method of using the bio-silica chip to detect interactions with biomaterials. The bio-silica chip will be very useful in biosensors, etc., because the bio-silica chip is advantageous in that it does not cause non-specific protein binding in the detection of protein-DNA, protein-ligand, protein-antibody, protein-peptide, protein-carbohydrate, protein-protein and cell-biomaterial interactions. Also, in the method for fabricating the bio-silica chip, a probe chip can be selectively immobilized on a silica device chip, which is widely used in biosensors, without a chemical surface treatment process. Thus, a chip fabricating process is simplified and a complicated process for purifying the probe protein becomes unnecessary, thus providing great improvements in productivity and economic efficiency.