Passive acoustic is considered to be a more economical and suitable method for long-term monitoring at sea. In this paper, a gas flow measurement method under low signal-to-ratio and overlapping conditions is proposed. The signal-to-noise ratio and measurement stability can be improved through complementary ensemble empirical mode decomposition and adaptive frequency matching. The normalized energy window is used to determine the time period of each bubble to ensure the accuracy of the frequency identification. The accuracy was verified by experiments. The results show that in the flow range of 100–1000mL/min, the measurement error is controlled within 6%. This paper provides insight into low signal-to-noise ratio and high-speed escaping gas flow measurement technology.