Gold nanoarray films prepared by glancing angle deposition are a new type of material with broad application prospects. Microstructure and thermal stability are of fundamental pertinence for corresponding practical applications, but there is a lack of systematic research at present. In this paper, pure Au nanofilms were prepared by glancing angle magnetron sputtering deposition. The three-dimensional morphology, texture, density, resistivity, and other parameters of the samples were quantitatively characterized with an atomic force microscope, an X-ray diffractometer, and a four-probe film resistance meter. Accordingly, the influence of the deposition glancing angle on the microstructure parameters was analyzed. Then the thermal stability of the film microstructure was studied. The microstructure of the Au films can be divided into three types in accordance with the oblique angle. When the glancing angle reached 60°, nanoparticle arrays began to form, whereas above 80°, nanorod arrays with a loose structure were formed. At 200 °C, the nanoparticle arrays degraded obviously in the form of surface flattening. For the nanorod arrays, the degradation temperature increased to 250 °C. In this process, the lateral size of the nanorods increased and their areal density decreased. The reason for the difference of thermal stability is that they have various microstructure features. Moreover, this structural distinction makes the micro mechanisms in the degradation process completely different.