Thinning of phased only rectangular planar array can reduce the cost and simplify the radio front end of the array. Therefore, it is reasonable to develop the thinning pattern synthesis approach for phased only rectangular planar array. In this letter, a novel computational approach is presented to form the beam pattern and thin the phased only rectangular planar array. First, a new simple matrix equation based on two-dimensional Fourier transform (FT) is derived to calculate the antenna element excitations and the beam pattern. Then, the computational steps to obtain the antenna element excitations with uniform amplitudes are presented. In order to increase the attenuation of the side lobes, the target beam pattern with varied phases determined by a novel analytical formula is proposed. Two examples are used to demonstrate the advantages of the new method. The simulation results show that the new approach can synthesize the beam pattern well, and the new pattern synthesis method has good performance in thinning the phased only rectangular array.