The main function of the substrate is to sustain and improve the performance of the thin-film. The property and surface configuration of the substrate material have a huge influence on the characteristics of the thin-film. Fabrication of substrate for the micro-transformer can choose a variety of materials, including the silicon, metal, glass, quartz, ceramics, plastics, polymer, etc. Different materials used as substrate have different effects on voltage gain and insertion loss of the transformer. At present, the silicon is used in most cases for its excellent properties. However, it is increasingly found that there exists some problems to gain better performance, such as the parasitic effect. And so, to employ other materials is essential. This paper discusses the effects induced by using different substrate materials. Through the analysis, a general cognition about how to choose the materials can be obtained, which is helpful to design and fabrication of the micro-transformer.