A fractional frequency transmission system (FFTS) is the most competitive choice for long distance transmission of offshore wind power, while the Hexverter, as a newly proposed direct AC/AC converter, is an attractive choice for its power conversion. This paper proposes a novel control scheme characterizing the global stability and strong robustness of the Hexverter in FFTS applications, which are based on the interconnection and damping assignment passivity-based control (IDA-PBC) methodology. Firstly, the frequency decoupled model of the Hexverter is studied and then a port-controlled Hamiltonian (PCH) model is built. On this basis, the IDA-PB control scheme of the Hexverter is designed. Considering the interference of system parameters and unmodeled dynamics, integrators are added to the IDA-PB controller to eliminate the steady-state error. In addition, the voltagebalancing control is applied in order to balance the capacitor DC voltages to obtain a better performance. Finally, the simulation results and experimental results are presented to verify the effectiveness and superiority of the IDA-PB controller.