In heat exchange fouling ultrasonic testing, the time-domain signal waveform often contains high aliasing due to small fouling thickness or high order echo interference, and so forth. This paper studies the method of acquiring time of flight from heat exchange fouling ultrasonic testing signal with high aliasing and presents the method that combined the Wiener deconvolution and high order cumulative spectrum estimation. For reference signal distortion problem, which may exist in real application, an iterative correction process is introduced in the form of Incremental Wiener algorithm. Simulation and experimental results show that the proposed method has better anti-noise ability, better time of flight accuracy and practicability.