In order to realize the fabrication of binary beam shaping element with complex phase structures, a new method of making the relief phase structures under the dot-by-dot exposure mode is presented by using laser direct writing (LDW) system with the square-spot. The size of the square spot obtained with the projection optical configuration is set to match with the minimum phase unit which lead to exposure mode can be easily controlled. The diffraction properties of the phase unit structures etched with single Gaussian spot and square spot are discussed. The binary beam-shaping elements with two-steps by square-spot exposure have been achieved to 31% +1 order diffraction efficiency. The experimental results are given.