The invention relates to a micro-array biochip, and a preparation method and an application of the micro-array biochip. The micro-array biochip comprises a glass chip substrate and a modification layer. The modification layer comprises a chromium layer, a silver and / or gold layer, a self-assembly monomolecular layer, and a photo-cross-linking agent and high-molecular layer, which are overlaid in sequential on the surface of the glass chip substrate. The invention also provides a protein micro-array, a method for preparing the protein micro-array, and an application of the protein micro-array to detect micromolecule medicine. According to the invention, three-dimensional high-molecular surface modification of the micro-array biochip is completed by the method, and the fixation amount of protein on the surface of the micro-array biochip can be effectively improved, so that micromolecule, hard to detect in the prior art, can be detected without marking, in accuracy, and in high flux. The micro-array biochip is of great significance to the field, such as molecular biology study and medicinal development.