Fractional frequency transmission system (FFTS), which is also known as low frequency AC transmission (LFAC), is a very promising transmission scheme for offshore wind farm integration. The protection of transmission line of FFTS is designed in this paper. Firstly, the characteristic of transmission line fault of FFTS is analyzed. Secondly, the protection is designed and the algorithms are introduced. Finally, the designed protection scheme is verified in MATLAB/Simulink and results show that the protection scheme performs well and is effective when fault occurs on transmission line of FFTS.