A method of controlling a washing machine includes rotating a motor for driving an inner shaft in a first direction, and aligning a clutch to a reference position corresponding to one of a maximum lowered position and a maximum raised position. The motor is rotated by a preset reference alignment angle in a second direction to align the clutch from the reference position to a starting position corresponding to one of an upper limit and a lower limit of a preset agitating control section. The upper limit of the agitating control section is spaced downward by a first distance from the maximum raised position, and the lower limit of the agitating control section is spaced upward by a second distance from the maximum lowered position. The motor is rotated by a starting alignment angle set according to a displacement of the clutch ranging from the starting position to a target position corresponding to the other one of the upper limit and the lower limit so that the clutch is moved from the starting position to the target position.