The invention relates to a compound control method for an array type electromagnet-permanent magnet system used for space microgravity ground-based simulation. A 26*26 electromagnet array is located at the bottom in the system. In consideration of the sizes of permanent magnets on a moving body and the working power of the system, under the circumstance that target precision is satisfied, a working region is a continuous 12*12 electromagnet array in a working process of the system, and the working region is switched according to position signals of the moving body. Because the moving body is an axially symmetric device, the horizontal position signal measured by the position detection signal represents the center position of the moving body, it is guaranteed that the center of the electromagnet array of the working region moves along with the axial center of the moving body through the array switching control algorithm, and the moving body nearly bears no force in the horizontal direction.