X-ray reflectivity and atomic force microscopy are two common tools in characterizing the surface roughness. However, the measurement results reported by these two methods were usually not consistent between each other. In this work, polished sapphire wafers with different surface roughness were prepared and measured by both methods. To understand the disagreement, a possible interpretation for X-ray reflectivity and atomic force microscopy on the characterization of the surface roughness is described. The difference in the X-ray reflectivity measurement, the X-ray beam covers a larger area of few mm2 on the sample, while the atomic force microscopy probes only a local area (around μm2). In general, the surface roughness measured by atomic force microscopy should be smoother than that obtained by X-ray reflectivity due to the convolution of tip shape of atomic force microscopy and the short wavelength of probing X-rays. However, the surface contamination of the sample and the atomic force microscopy environment complicate the measurements for both methods, especially, for these samples with root-mean-square roughness less than 1 nm.