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Three-dimensional imaging radar based on thinned array is investigated in the paper. The multiple phase center aperture synthesis method in time division mode is used to eliminate the high side lobes of thinned array. Using simulated annealing algorithm to optimize the location of antennas, so as to minimize the number of antennas used. Combined with motion compensation, the synthesized phase centers both in quantity and distribution are coincident with a full array. For the cross-track array length is far smaller than the scene width, three-dimensional imaging method is employed with sub-aperture imaging along cross-track. The simulation results denote the validity of the method proposed in the paper.