Terahertz(THz) Microstrip Line(MSL) is the key to THz system on chip. The rationality of the design of THz MSL affects the sensitivity and accuracy of THz on-chip system directly. To make the on-chip system better, the THz MSL and the MSL band stop filter were simulated by using the software HFSS(High Frequency Structure Simulator) by reference the theoretical model. The transmission characteristics of THz MSL and the MSL band stop filter were researched by simulation. From the point of view of application, the sample, such as GaAs, was introduced into the simulation model to research the effect of GaAs sample on the filter characteristic of band stop filter for first time. Finally, a 358 GHz MSL band stop filter was designed, and the effect of GaAs sample on the center frequency of band stop filter was discovered by changing the size of the GaAs sample putting on the band stop filter. The results of this paper provide accurate theoretical data for the design and fabrication of THz MSL.