We report the effects of the substrate temperature on the surface morphology of Molybdenum tri-oxide (MoO3) thin films and the electrically detailed examination of Au/MoO3/n-GaAs MOS heterojunction structure with the best homogeneity. MoO3 thin film was deposited both on soda-lime silicate glass as a thin film and n-type and (100) oriented GaAs substrates using RF magnetron sputtering method at substrate temperatures of room temperature, 100 degrees C, 200 degrees C and 300 degrees C. Surface morphology of the MoO3 thin films were investigated by utilizing atomic force microscopy (AFM) and scanning electron microscopy (SEM) measurements. AFM and SEM results have shown that MoO3 thin film with substrate temperature of 200 degrees C has the lowest surface roughness and the homogeneity of the film structures significantly enhances with increasing substrate temperature up to 200 degrees C. An inclement in roughness of thin film structure was detected at higher temperature than 200 degrees C due to the deterioration of homogeneity. Therefore, we primarily focused on the MoO3 thin films produced at the substrate temperature of 200 degrees C to examine the electrical properties of Au/MoO3/n-GaAs MOS heterojunction device. In order to determine the electrical properties, temperature dependent I - V measurements were performed in between 200 and 400 K by steps of 25 K. The fundamental electrical parameters such as saturation current (I-0), ideality factor (n), and barrier height (phi(0)) were calculated by analyzing the forward bias I-V curves at different temperatures. The series resistance (R-s) values of the device were also determined using the plot of structure resistance (R-i) vs applied bias voltage (V-i), Thermionic Emission Theory and Cheung and Cheung methods. The R-s value of Au/MoO3/n-GaAs MOS heterojunction device shows an abnormal behavior of up to 350 K, which is the critical temperature value and tends to increase with increasing temperature. Above the critical temperature value, it exhibits ideal behavior.