In this study, liquid crystal (LC) aligning properties for homeotropic alignment on the $SiO_x$ thin film by electron beam evaporation method with electron beam system in accordance with the evaporation angles were investigated. Also, the control of pretilt angles homeotropic aligned LC on $SiO_x$ thin film as the function of the evaporation angles were studied. The uniform vertical LC alignment on the $SiO_x$ thin film surfaces with electron beam evaporation was achieved with all of the thin film angle conditions. It is considerated 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. The values of the pretilt angles according to the evaporation angle were from about $0.7^{circ}$ to about $3.4^{circ}$. The highest pretilt angles of about $3.4^{circ}$ in aligned NLC on the $SiO_x$ thin film surfaces by electron beam evaporation were measured under the condition of $45^{circ}$. Also, good LC alignment states on the treated $SiO_x$ thin film layer by electron beam evaporation were observed at annealing temperature of $250^{circ}C$. Consequently, the high pretilt angle and the good thermal stability of LC alignment on the $SiO_x$ thin film by electron beam evaporation can be achieved.