The surface profile is of importance to the output characteristics of the waveguide optical phased array. The far field diffraction model of the array with an uneven surface was established based on the coherent superposition principle. The general formulas of the far optical field distribution were derived using the model. The effects of the surface profile on the output wave phase and the phase on the far optical field distribution were analyzed. When the surface profile was a inclined surface, a concave one, the single depression and the random fluctuation, the output light intensity was researched respectively. The results show that the surface profile has a great influence on the output far optical field and the position and intensity of the main lobe will be changed partly. These will affect the accuracy and power of the scanning beam and is of importance to the application of the waveguide optical phased array.