The invention discloses a topological map based unmanned boat route searching system and method. The method comprises following steps: step one, obtaining the external information of the searching area of an unmanned boat, wherein the external information comprises data of start position, final position, number of barriers, and edge point sets of barriers, based on the external information, carrying out route information analysis, based on the analysis result, establishing navigation topological relationship of the unmanned boat, and based on the topological relationship, establishing a spatial topological map; and step two, based on the established spatial topological map, a Dijskra algorithm, and navigation conditions of the unmanned boat, calculating the optimal path, and after the optical path is selected, controlling the track of the unmanned boat according to the optimal path. The method has the advantages that the optimal path that can meet the navigation requirements can be calculated out, the algorithm complexity is reduced, and the situation that route searching is trapped by local optimum is avoided.