Secondary electron emission (SEE), which is a frequent phenomenon in space high power microwave systems, is one of the basic inducement of multipactor in space microwave components. It is already verified that lowering SEE is an effective method to mitigate the undesirable effect. Metal black nanostructures have ever been reported to suppress SEE remarkably, however, the SEE characteristics of the gold nanostructures are rarely investigated. In this work, we use the thermal evaporation to fabricate the gold nanostructures under various evaporation gas pressures, and further analyze their SEE characteristics as well as energy distribution information. Experimental results reveal that the evaporation gas pressure determines the morphology of gold nanostructure, and the morphology dominates the SEE level of the gold nanostructure. To be specific, as the evaporation gas pressure rises, the porosity of the nanostructure increases and the SEE yield decreases. The energy distribution information indicates that the gold nanostructure just suppresses the true secondary electrons (TSEs) effectively. However, the effect of the nanostructure on the back scattered electrons (BSEs) is heavily dependent on the surface morphology. Specifically, the nanostructure fabricated at 70 Pa suppresses the BSEs weakly while the nanostructures fabricated at 40-60 Pa enhance the BSEs to some degree. To theoretically explain the experimental phenomena, we establish an equivalent model, which is made up of the periodical combination of a hemisphere and a composite groove, to imitate the fabricated gold nanostructure and simulate its SEE characteristics based on the SEE phenomenological probability model. Simulation results indicate that the hemisphere induces more TSEs and BSEs while the composite groove suppresses them, besides, the groove suppresses the TSEs much more remarkably than the BSEs. The SEE level of the nanostructure model is determined by the weighted average effect of both the hemisphere and the groove. The simulations qualitatively explain the experimental phenomena. This work in depth reveals the SEE mechanism for the gold nanostructures, and is of considerable significance for developing the low SEE surface on a nanometer scale in a space high power microwave-system.