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 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 an adjusted location based on the matched edge for a control unit to display the adjusted location on the device.