A dual-layer alignment apparatus is disclosed which includes: a fixed frame (40) and, disposed thereon, a first measuring device (50) and a mark plate (41), the mark plate (41) having a fixed-frame mark (20); and a motion stage (60) and, disposed thereon, a reference mark (30), a motion-stage mark (70) and a second measuring device (10). The first measuring device (50) is configured to measure a relative positional relationship between the reference mark (30) and the motion-stage mark (70), the second measuring device (10) is configured to measure a relative positional relationship between the reference mark (30) and the fixed-frame mark (20), from which a final relative positional relationship between the motion-stage mark (70) and the fixed-frame mark (20) is derived, based on which the motion stage (60) is displaced to a target location. A corresponding dual-layer alignment method is also disclosed. In the apparatus, the motion stage (60) is the only movable component. Additionally, coordinate relationships can be calibrated in a static manner in order to immunize calibration accuracy from positioning accuracy of the motion stage (60), such that the alignment accuracy is improved. Further, a dual- or multi-lens design can be employed to allow additional improvements in flexibility and alignment efficiency.