A discrete probability distribution function is used to represent the squared transverse roughness effect in a modified Reynolds equation, and the Reynolds equation is used to calculate the hydrodynamic lubrication in a slider-disk interface compared to the CFD method. When the roughness height is below 1% of the film thickness, the results acquired by the two methods are the same and the surface roughness does not show obvious effect on the lubrication results compared to that on the smooth surface. The load capacity and friction force increase as the roughness height increases when the roughness height exceeds 1% of the film thickness. Moreover, the forces acquired by Reynolds equations are smaller than those acquired by CFD, and the difference between them exceeds 10% when the roughness height is higher than 10% of the film thickness. Sidewall effect is considered to be the main reason for the difference, and the Reynolds equation is believed not suitable for calculating the effect of the squared transverse roughness in the hydrodynamic lubrication.