To improve the flutter stability of a long-span suspension bridge with double-decks, aerodynamic optimization on the upper and lower bridge decks is studied, and a series of countermeasures are considered, including slotted deck, wind fairings, porosity of guardrail, and horizontal and vertical stabilizers. Wind tunnel tests were performed to measure the critical flutter wind speed of the bridge and find effective aerodynamic countermeasures for improvement of the flutter stability. The results show that double-vertical stabilizers symmetrically installed at the two sides of the bottom of the lower deck with the distance of 9.32 or 11.55 m to the center efficiently improve the flutter performance of the original section at 23°, 0°, and 3°angles of attack simultaneously, while other common aerodynamic measures can hardly achieve this effect alone. The composite measure which consists of two central stabilizers installed on the top of the upper and lower decks, respectively, is promise and superior to the single measure. The combination of wind fairing and central stabilizer on the top of the lower deck is also an effective countermeasure. The results can provide the reference information for flutter optimization of the long-span steel truss girder suspension bridge with double-deck in the future.