Several technologies can be used in ultrasonic gas flow-meters, such as transit-time, Doppler, cross-correlation and etc. In applications, the approach based on measuring transit-time has demonstrated its advantages and become more popular. Among those techniques which can be applied to determine time-of-flight (TOF) of ultrasonic waves, including threshold detection, cross correlation algorithm and other digital signal processing algorithms, cross correlation algorithm has more advantages when the received ultrasonic signal is severely disturbed by the noise. However, the reference wave for cross correlation computation has great influence on the precise measurement of TOF. In the applications of the multipath flow-meters, selection of the reference wave becomes even more complicated. Based on the analysis of the impact factors that will introduce noise and waveform distortion of ultrasonic waves, an averaging method is proposed to determine the reference wave in this paper. In the multipath ultrasonic gas flow-meter, the analysis of each path of ultrasound needs its own reference wave. In case study, a six-path ultrasonic gas flow-meter has been designed and tested with air flow through the pipeline. The results demonstrate that the flow rate accuracy and the repeatability of the TOF are significantly improved by using averaging reference wave, compared with that using random reference wave.