This study presents an investigation into the control of an axial-flux permanent magnet synchronous machine (PMSM) with contra-rotating rotors fed by a single inverter, which corresponds to two PMSM connected in series. In this study, the mathematic model of the PMSM with contra-rotating rotors is developed and the instability of the system with unbalanced loads is analysed. Based on the analysis, a control strategy which can keep synchronism of the two rotors under varying load is implemented. In addition, a method for starting the motor reliably is proposed, which is applicable to ship or under water vehicle propulsions. The control strategy is implemented on a DSP 28335 processor featured hardware platform and is tested on a 1.2 kW prototype machine. Experimental results validate the correctness of the analysis and control strategy.