The coordination of directional overcurrent relays considering different topologies is an essential fundamental work for overcurrent relays applied to the power grid projects. In order to solve the problem of difficulty in solving the model of optimal coordination of relays and the poor performance of the obtained relay settings after taking into account different network topologies, a novel method for optimal coordination of directional overcurrent relays under different topologies based on topology grouping and equivalence is proposed. Based on the established network topology description model suitable for relay coordination, the different network topologies are clustered by using the aggregation hierarchical clustering algorithm. The equivalent representative topology of each topology cluster is obtained by calculating the topological trajectory similarity. The model of optimal coordination of directional overcurrent relays based on equivalent representative topology is finally established to determine the relay settings. The results of the case study of the IEEE 30-node power system show that the proposed method effectively can reduce the constraint dimension and guarantee the performance of the obtained relay settings towards different network topologies.