The invention relates to the field of semiconductor micro-nano manufacturing processes, in particular to atomic layer deposition equipment and method for two-dimensional film patterning manufacturing. The core of the preparation method is that a bearing platform in a deposition cavity is replaced by a multi-station rotating disc, the disc is provided with a plurality of double-layer stations in the circumferential direction, the upper layer is used for fixing a patterned mask, and the lower layer is used for fixing a deposition substrate; and an external control system drives the disc to rotate step by step, so that the stations sequentially enter a central deposition reaction area, and flexible definition of two-dimensional material film deposition of atomic deposition on the surface of the substrate and a preset pattern is realized in cooperation with alternate pulses of a precursor source. The structure supports the design of various patterning masks and multi-substrate continuous processing, and the flexibility and the process efficiency of patterned film preparation are remarkably improved.