The invention discloses a method for preparing a multi-level structural microarray by a laser direct-writing technology, and belongs to the field of laser micromachining. In an array preparation process, a plane geometry structure is determined by plane figures input into a computer; the resolution depends on the multiple of a microfilm lens in a light path and the precision of a nanomotor and can reach 0.3 mu m; and based on the relationship between exposure depth and exposure time and the relationship between development depth and development time obtained by an experiment, the depth of a machining size is controlled by the regulation and the control of the exposure time and the development time. The method does not need a mask or a photolithography model, greatly reduces the preparation cost of arrays, has the feasibility of preparing a multi-level structure and high efficiency, and is suitable for the popularization of industrial production.