Thyristor Controlled Phase Shifter (TCPS) can control the power flow distribution by adjusting phase-shifting angle, and enhance the economy of power grid. But the application of TCPS changes the structure of power grid and the coupling relationship between phases. In this case, some key issues have to be considered while using pilot protection on transmission lines with TCPS, which include the installation of current transformer, the effects of phase shift angle on differential current calculation and the characteristics of traditional direction component. This paper introduces the principle of TCPS and builds a simulation model in PSCAD, and analyzes characteristics of the directional component and differential component considering the transmission lines with TCPS. The simulation results show that the directional pilot protection can be applied in transmission lines with TCPS, but for the current differential protection, it is best to use current transformers installed at the line side.