A structure of a dual exhaust system for a cylinder deactivation (CDA) engine, may include two inlet pipes, two outlet pipes, each of which protrudes and extends from an inside of a corresponding main muffler to an outside of the corresponding main muffler, wherein each of the two outlet pipes releases the exhaust gas passing through the corresponding main muffler to an outside of the vehicle therethrough, a connecting pipe disposed in a vehicle width direction and connecting between the two main mufflers, and a valve mounted on one outlet pipe of the two outlet pipes to open and close the one outlet pipe, wherein when the valve may be closed, the exhaust gas passing through one of the main mufflers may be introduced into the other main muffler of the two outlet pipes through the connecting pipe and then may be emitted to the outside of the vehicle.