The invention provides a deep ultraviolet laser and photo-emission electron microscope docking system comprising a vacuum sealed pipeline, a second flexible sealed pipeline, an incident lens and a first flexible sealed pipeline which are connected in sequence. The vacuum sealed pipeline is used to connect a deep ultraviolet laser, and the first flexible sealed pipeline is used to connect a photo-emission electron microscope. According to the invention, the lateral side of the first flexible sealed pipeline and/or the lateral side of the second flexible sealed pipeline are/is additionally equipped with an adjusting mechanism, so that one-dimensional adjustment of an incident window along the axial direction and two-dimensional adjustment of the incident window along the tilt angle direction are realized through matching between the adjusting mechanism and the first flexible sealed pipeline and/or the adjusting mechanism and the second flexible sealed pipeline. Therefore, the problem that the tilt angle deviation caused by assembly error cannot be adjusted in the prior art is solved, and sample alignment through laser is facilitated.