This paper proposes a control method of the whole ship Integrated Power System (IPS) with an Active Front End (AFE) converter and a Battery Energy Storage System (BESS). The propulsion inverter which drives the propulsion motor controls the ship speed by controlling the torque of the motor. The AFE converter controls not only the active and reactive power flow at the Point of Common Coupling (PCC) to suppress the transients of the both frequency and voltage of the PCC simultaneously, but also the State Of Charge (SOC) of the BESS. The components of the ship IPS are modeled partially by software or implemented partially as hardware for the real time Power HardwareIn-the Loop Simulation (PHILS) to verify the proposed algorithm. The parallel operating generators and their associate controllers, ship-service load, and pulse load are modeled in C code, after partitioned to distributed computational burden, and simulated in low cost multicore DSP. The hardware is down scaled because of the cost, time, space and safety issues while preserving the electrical and mechanical dynamics. The connection between HILS and hardware is achieved via a custom designed voltage amplifier. The dynamics and load sharing properties of the parallel operating generators, the proposed propulsion inverter controller, and the AFE converter controller have been verified successfully.