Abstract: In order to obtain terahertz isolators with simple structure and without the need of additional low temperatures and strong magnetic fields, a silicon-based photonic crystal heterostructure THz isolator was ananlyzed and optimized by using three-dimensional finite-difference time-domain method (3-D-FDTD). The isolator can work at room temperature, with simple structure and without external magnetic field. The results show that the isolation characteristics depends on the ratio of the pore size of both the photonic crystals. In the right ratio of the aperture (optimized aperture ratio R1/R2=0.49 at 0.52THz),maximum isolation of 25dB can be achieved.