Multilayer thin films with 2.3 nm-7.6 nm of d-spacing were deposited on fusion glass and float glass substrates by magnetron sputtering. Multilayer thin film with a lower interface roughness was deposited at an abnormal discharge region of I-V characteristic curve in DC glow discharge, compared to normal discharge region. Interface roughness of periodical multilayer in general depends on layer thickness, but in this study interface roughness was controlled by adjusting deposition conditions regardless of layer thickness. But interface roughness and X-ray reflectivity (XRR) of multilayer react sensitively to surface roughness of substrate. Multilayer thin film with 2.3 nm d-spacing shoes 42% of characteristic X-ray reflectivity(Cu Kα, λ=~0.154 nm), while 3.6 nm d-spacing shows 80% of reflectivity. XRR, transmission electron microscope (TEM) and atomic force microscopy (AFM) were used to analyze the interface roughness (σ), surface roughness and d-spacing.