Ultrasonic flowmeter has been widely used in chemical industry, metallurgy, and oil industry due to the advantage of highly accurate, non-invasive, and no pressure loss nature. However, in some harsh measurement scenarios like in hydrogen recycling loop and downhole energy fluid transportation, it may lack the accuracy to resolve small flow rate change. Traditional Time-Of-Flight (TOF) estimation methods used in ultrasonic flowmeters tend to show low accuracy and lack of robustness in these scenarios which often tend to show low signal-noise ratio and with a lot of noise interference. So, the key factor is the TOF estimation accuracy. To solve this problem, we propose the central frequency matching method. With the use of segmentation, signal filtering, and time-frequency analysis, it can provide TOF estimation accuracy and noise robustness. According to the experimental study, the proposed method makes good use of the characteristics of ultrasonic flow meters, improves the accuracy and reduces the error, and effectively broadens the applicable scenarios of ultrasonic flow meters.