A control device for a watercraft propulsion system can reduce wear of a shift mechanism, can achieve an automated extremely slow speed navigation and easy watercraft navigation, and can negate differences between watercraft navigation skills of watercraft operators. A remote control operation section includes a remote controller shift lever. A watercraft propulsion section includes a shift change unit and a shift actuator arranged to drive the shift change unit, a main control section arranged to control an operation of the shift actuator based upon an operational amount of the remote controller shift lever, an auxiliary control section arranged to control a watercraft to move at an extremely slow speed, and a changeover section arranged to select one of the main control section and an auxiliary control section. The auxiliary control section includes a data table for moving a watercraft hull at an extremely slow speed, and the auxiliary control section outputs an execution instruction of extremely slow speed navigation to the shift actuator by selecting one of extremely slow speed navigation instructing data from the data table.