Flutter wind tunnel test is an important approach of investigation of transonic flutter characteristics of flight vehicle. Comparing with the blow-down wind tunnel, the long-running and low dynamic pressure capabilities of continuous transonic wind tunnel are very suitable for flutter test. The flutter safety protection and analysis of dynamic signals are developed. The safety protection control software, rapid reduction of Mach number and dynamic pressure, model debris catch screen are integrated, which can provide safety protection of test model and wind tunnel. During the test process, the flutter boundary can be achieved by interpolating the reciprocal of spectrum peak. The flutter tests of rudder are conduct through two methods of step and continuous varying dynamic pressure. It is illustrated that the error of flutter dynamic pressure is relatively small, less than 5% between the two methods. Meanwhile, the feedback effect of the real servo actuator on the flutter characteristics is hard to be obtained via numerical simulation. It is demonstrated that the flutter dynamic pressure has been increased by 10% due to the feedback effect.