The invention discloses a rapid flexible mechanical beam end positioning algorithm for point-to-point small displacement translation. The algorithm comprises: S1, a vibration period T0 of mechanical beam is calculated; S2, time of one period for point-to-point motion is divided into n equal parts equally, wherein the value of the n is equal to T0; S3, a speed vi at each equal part point is calculated; S4, the number Wi of pulses sent by a servo motor is calculated; and S5, interpolation computation of the pulse number Wn at the last equal part point n is carried out. Therefore, the system controller becomes simple and the operation becomes easy and reliable; because no extra hardware structure needs to be added, the system cost is reduced correspondingly and the post maintenance becomes easy. The algorithm can be widely applied to system equivalent to the flexible beam structure; and rapid and accurate positioning control of the point-to-point displacement translation can be realized.