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The transit time of a thermal signal traveling along with a liquid flow can be obtained using a cross-correlation method. This transit-time-based flowmeter using thermocouples with grounded stainless steel shielding is by far the most robust and reliable solution to measure the flow rate in a harsh environment of high temperature, irradiation, and corrosion, typically seen in a nuclear reactor. In practice, cross-correlation calculation tends to produce flat peak plateau or multiple peaks, leading to a significant error in peak detection. To overcome this problem, in this paper, an autoadaptive impulse response function (AAIRF) estimation technique is thus introduced, and a significantly narrower peak is shown theoretically and also verified experimentally. In addition, we show that more accurate results can be obtained if a moving-average-filter-based cross-correlation function is combined with AAIRF. In this paper, we also investigate a few important practical problems related to negative delays and sampling frequencies of the data acquisition.