The use of green energy to power ships in the marine industry has attracted increasing attention in recent years. This paper presents an inland river cruise ship supplied by a fuel cell (FC) as the main power source and a supercapacitor (SC) as the auxiliary power source. Its propulsion inverter adopts the proposed high-boost Z-source inverter, and the proposed high-voltage-boost Z-source inverter (HVB-ZSI) principle is studied. The advantages of this proposed HVB-ZSI in two cases are verified through simulation. In case 1, it can be seen that the capacitance voltage is only 250 V, and the maximum inductance’s inrush current at the start is less than 200 A. But the capacitance voltage of HVB-ZSI reaches 383 V, and the inrush current is 300 A. While considering different constraints of the propulsion system, four operating modes for the set of the FC and SC are proposed. The small-signal model of the propulsion system is derived, and the control strategy is studied. By controlling the shoot-through duty cycle and modulation factor, the FC power, output power, and state of charge (SOC) of the SC can be controlled. Finally, to verify the performance of the proposed propulsion system, a hybrid power ship prototype equipped with a 7.5 kw propulsion motor is constructed. Four modes of the entire system are simulated by MATLAB/SIMULINK, and its performance is analyzed with experimental results. These results show that the new Z-source propulsion system has a promising application in new energy ships, as it has higher reliability and lower complexity and cost compared to conventional propulsion systems.