Electrical resistivity in amorphous Mg65Zn30Ca5 thin films with thicknesses ranging from 49 nm to 1786 nm is investigated by four-probe method at 4-300 K. It is revealed that for thickness from 94 nm to 1786 nm the Ziman-Faber diffraction model can describe temperature-dependent electrical resistivity, while for 49 nm-thick film the two-level system scattering mechanism is validated below 40 K and Ziman-Faber diffraction model above 40 K. More interface fraction between the columnar structures with enhanced heterogeneity could be the possible origin of two-level system scattering in thinnest film, instead of denser atomic packing.