The invention discloses an elephant trunk method-based anti-blocking dredging system and a construction method thereof. The system comprises a probing and dredging device; the probing and dredging device comprises a case, a hoop type ring and a handheld end control device; the case is provided with a detector, and the bottom of the case is provided with an electric vibrating rod; one end, far away from a sleeve opening, of the hoop type ring is connected to the bottom of the case, a mounting hole for an elephant trunk to penetrate through is formed in the inner side of the ring, and a plurality of electric rollers are movably mounted in the mounting hole; and the handheld end control device is electrically connected to the electric vibrating rod, the electric rollers and the detector. The matched probing and dredging device is installed on the elephant trunk and moves along the elephant trunk through manual rope traction operation or complete remote control operation, a specific pipe blocking position is probed through an elephant trunk opening and a camera, and the vibrating rod is remotely operated to rotate to a proper position for vibrating and dredging; and pipe disassembly dredging and high-altitude operation are avoided, safety is guaranteed, meanwhile, construction is convenient, cost is saved, and the construction period is shortened. The dredging system is easy and convenient to operate, high in applicability, facilitates the application and popularization of the elephant trunk, and greatly improves the construction efficiency of deep foundation pits and mass concrete.