A marine vessel propulsion system includes first and second propulsion devices, a first operation lever arranged to be operated by a marine vessel maneuvering operator to control the first propulsion device, a second operation lever arranged to be operated by the marine vessel maneuvering operator to control the second propulsion device, a first lever position sensor arranged to detect a position of the first operation lever, a second lever position sensor arranged to detect a position of the second operation lever, and a control unit. The control unit is programmed to set a target pivoting speed according to the positions of the first and second operation levers relative to each other and set a target travel speed according to amounts of displacement of the first and second operation levers with respect to neutral positions.