In practical applications of dielectric barrier discharges under atmospheric pressure, plasma usually acts on non-smooth surfaces. The electric field distortion and uneven surface charge distribution caused by its surface morphology will create an adverse effect on the uniformity and stability of the discharge. In this paper, we establish a simulation model of atmospheric pressure helium dielectric barrier discharge on a wavy lower dielectric plate, and use a sinusoidal clipping voltage to regulate the discharge uniformity. The results show that the discharge uniformity is improved compared with the unclipped case, and the discharge mode is changed from columnar mode to quasi-uniform mode. This can be attributed to the incomplete discharge dissipation caused by the reduction of air gap voltage; the subsequent electron backflow process neutralizes the the residual space electrons with the surface charge, which limits the accumulation of surface charges. With the increase of clipping ratio, the surface charge distribution becomes more uniform, and the radial fluctuation of electric field distribution weakens. In addition, the discharge efficiency is improved in a certain clipping range. This study reveals the mechanism of clipping voltage influence on non-smooth surface discharge, and provides a new idea for regulating the uniformity of dielectric barrier discharge.