To provide a method for manufacturing a substrate for making a microarray which will ensure the secure immobilization of a material in a site-selective manner at a low cost. The method comprises the steps of: forming a monomolecular film on the surface of a substrate using a silane compound represented by the following general formula (1), Y3Si—(CH2)m—X  (1), wherein m represents an integer from 3 to 20; X represents a hydroxyl group precursor functional group which will be converted to a hydroxyl group when exposed to acid; and Y independently represents a halogen atom or alkoxy group having 1-4 carbon atoms; and converting the hydroxyl group precursor functional group represented by X to a hydroxyl group; wherein the step of converting a hydroxyl group precursor functional group represented by X to a hydroxyl group comprises forming, on the monomolecular film, a polymer layer containing a compound represented by the following general formula (2) or (3),