The invention discloses a three-dimensional carrier of a microarray biochip and a preparation method thereof. The three-dimensional carrier of a microarray biochip is prepared by growing a zinc oxide nanorod on the surface of a substrate material and growing a polymer brush on the surface of the zinc oxide nanorod. The preparation method comprises the following steps of: activating the surface of the substrate material, and growing a zinc oxide nanorod on the surface of the substrate material; performing surface modification on the grown zinc oxide nanorod; connecting the modified surface of the zinc oxide nanorod with an initiator; and finally, growing a polymer brush to obtain a three-dimensional carrier of a microarray biochip. The preparation method is simple, does not need special equipment, has low production cost and good repeatability, and can be used for realizing large-scale production; the prepared three-dimensional carrier has low price and high fixing density for probe molecule, can be used for effectively inhibiting non-specific protein adsorption and improving the sensitivity and the specificity, and can be widely applied to the fields of biology, basic medicine, disease diagnosis, drug screening, food safety, environmental monitoring and the like.