Waveguides, which can transmit high frequency electromagnetic waves, have a lot of types, such as microstrip line (MSL), coplanar waveguides (CPW), coplanar-strip-line (CPS) and so forth. In the waveguides mentioned above, CPW has the advantages of easy fabrication and superior performance. Meanwhile MSL also has many advantages such as small size, light weight and high spectral resolution, but it also shows a higher attenuation and dispersion compared with the free-space waveguides. So in on-chip terahertz system, CPW and MSL was used as waveguides to transmit terahertz waves and the HFSS software was used to simulate and analyze the transmission characteristics of the MSL and CPW based on the on-chip system researched by University of Leeds (America) and Hiroshima University (Japan). The simulation results show that the scattering parameters of the two waveguides are similar to the known literatures. Meanwhile we also have designed a new structure of MSL which is applicable for our on-chip system.