The electrical characteristics and the microstructure of Mo/GaAs Schottky diodes fabricated by electron-beam evaporation have been studied. The barrier height, ideality factor, deep trapping levels and intermetallic compounds of these annealed or unannealed Mo/GaAs Schottky diodes are obtained by using the I-V, C-V, Rutherford backscattering spectroscopy (RBS), Auger electron spectroscopy (AES), deep level transient spectroscopy (DLTS) and transmission electron microscopy (TEM) analyses. An obvious interdiffusion at Mo/GaAs interface is observed in Mo/GaAs Schottky diodes annealed above 500°C for 10 min. DLTS results show that there are two electron traps [Ec-(0.52±0.02)'eV and Ec-(0.86±0.02) eV] and one hole trap [Ev+(0.92±0.02) eV] are demonstrated for 300°C, 400°C post-annealed Mo/GaAs diodes. TEM results also indicate that the disappearance of these deep trapping levels may correlated to the formation of intermetallic compounds GaMo3 and MoAs2 existed in Mo/GaAs diodes post-annealed above 500°C. It is believed that the metal-semiconductor interdiffusion and the intermetallic compounds play the major roles for the thermal degradation of Mo/GaAs Schottky diodes.