The invention discloses a long shaft deep well pump applied to the high-speed rail drainage engineering and with a sand prevention function. The long shaft deep well pump comprises a protection cover, and the protection cover is of a cylindrical structure and provided with a first through hole; the first through hole is internally provided with a transmission shaft, one end of the transmission shaft is provided with a coupler, the end, away from the transmission shaft, of the coupler is connected with a motor, and the motor is fixed to the position above the protection cover; the side, close to the motor, of the interior of the protection cover is provided with a bearing seat, the bearing seat is provided with a first bearing, and an inner ring of the first bearing is in cup joint with a transmission shaft; the end face, away from the motor, of the protection cover is provided with an installation plate, the side edge of the installation plate is provided with a second through hole, and the second through hole is internally in cup joint with the transmission shaft; and the end, away from the motor, of the transmission shaft is connected with a power shaft, and the end, away from the transmission shaft, of the power shaft is provided with a suction type impeller. By means of the long shaft deep well pump, the directional drainage purpose is achieved, pipeline crossing is avoided, under the condition of guaranteeing that the bottom is stable while the purpose of filtering is achieved, and the situation that silt enters a pump body to cause blocking is effectively avoided.