Heat exchangers are the most important equipment in ship cooling system, which generate vibration and noise due to flow excitation during operation, affecting structural safety and having a significant impact on acoustic stealth performance. Mastering the characteristics of sound source has guiding significance for noise reduction design. The acoustic signal directly obtained from the hydrophone inside the pipe including reflected sound wave, which cannot accurately characterize the sound radiation energy from heat exchanger into pipe. In order to accurately evaluate the sound source characteristics of heat exchanger under flow conditions, experimental method was used to test the sound source characteristics of heat exchanger which are not affected by connected pipelines based on the two-port sound source theory. The main factors affecting the sound source characteristics of heat exchanger were analyzed, such as flow rate, background pressure, and temperature. The research can provide reference for the vibration and noise reduction design of heat exchangers.