The invention discloses a topology discovery system of a next generation Internet based on the IPv6 (Internet Protocol Version 6), comprising a detection list input module, an equipment and connection relation discovery module, an equipment and subnet topology discovery module, an analysis integration module, a topology structure information storage module, a database and a topology structure information display module. The invention also discloses a realizing method of the system, comprising the following steps: (S1) forming a detection node list by the detection list input module; (S2) sending a network path detection packet by the equipment and connection relation discovery module to acquire a router marked by an IPv6 address and a connection relation thereof, and exchanging network topology information between the equipment and subnet topology discovery module and the router on the network to acquire the network topology information; and (S3) analyzing by the analysis integration module to form an integrated topology structure diagram. The invention has the advantages of enhanced stability, better performance, alias removal, and the like and effectively improves the accuracy and the integrity of topology discovery.