The invention relates to a drive system and control method for a boat tractor. The drive system comprises a main gearbox and wheel reducers matched with the main gearbox through spline sleeves and connecting sleeves; the wheel reducers are two and symmetrically arranged on two sides of the main gearbox, and the two wheel reducers are identical in structure; and the main gearbox includes an outer shell, brakes arranged in the outer shell and used for controlling combination or separation of the gearbox and the wheel reducers, a plurality of drive shafts, a power input shaft, a power output shaft, and a plurality of gears connected with the brakes, the plurality of drive shafts, the power input shaft and the power output shaft. The drive system and control method provided by the invention have the following advantages: a walking system of the boat tractor, power output of rotary tilling farm implements, power output of an oil pump, steering and braking are integrated, and the system hasa compact structure, is convenient for installation, and has reliable use.