1. A method of operation of a navigation system comprising: receiving a current position for locating a device; adding a new edge from a road topology map to a topological tree based on an edge of the road topology map corresponding to the current position, wherein: the road topology map is for representing segments of real-world vehicle pathways, the topological tree is for dynamically representing a set of edges in the road topology map corresponding to the current position; removing an old edge outside of a termination condition with no descendant edges within the termination condition from the topological tree based on the current position; determining a matched edge of the topological tree based on the current position and the topological tree; and calculating with a control unit an adjusted location based on the matched edge for mapping the current position to the adjusted location on the matched edge.