In this study, liquid crystal(LC) aligning capabilities for homeotropic alignment on the $SiO_x$ thin film by electron beam evaporation method were investigated. Also, the control of pretilt angles and thermal stabilities of the nematic liquid crystal(NLC) treated on $SiO_x$ thin film were investigated. A high pretilt angle of about $86.5^{circ}$ was obtained, and also the suitable pretilt angle of the NLC on the $SiO_x$ thin film at $10{sim}50nm$ thickness with e-beam evaporation can be achieved. The uniform LC alignment and good thermal stabilities on the $SiO_x$ thin film surfaces with electron beam evaporation can be achieved. It is considered that the LC alignment on the $SiO_x$ thin film by electron beam evaporation is attributed to elastic interaction between LC molecules and micro-grooves at the $SiO_x$ thin film surface created by evaporation.