The invention relates to a method for automatically arranging a photovoltaic array in a complex terrain. The method comprises the steps of (1) calculating amount of solar radiation according to the current latitude so as to calculate an optimum tilt angle; (2) carrying out preliminary division on a given region; (3) carrying out occlusion calculation so as to calculate a shadow area, marking the calculated shadow area, and adjusting areas obtained in the step (2); (4) performing photovoltaic array grid division on the area to be arranged, and carrying out initial arrangement; (5) performing inverter grid division on the area to be arranged; (6) determining the arrangement positions of an inverter and a combiner box. In the steps (1), (2) and (3), the tilt angle and initial area to be arranged of the photovoltaic array are determined, and the arrangement of the photovoltaic array is well prepared; on this basis, the comprehensive optimal arrangement of the photovoltaic array is realized by means of the steps (4), (5) and (6).