Abstract: Ultrasonic measurements are mostly based on the determination of the transmission time of waves, the measurement accuracy of transmission time directly impacts the final detection accuracy. The traditional phase difference measurement of transmission time only considered the error by Gaussian noise, based on this, the influence of A/D quantizing error was considered. Using error theory, the sine signal A/D quantizing error was deduced, and the final root mean square (RMS) formula of total error was presented. For the two cases that the ultrasonic frequency was known and known, the method of phase difference based on fast Fourier transform (FFT) and the method of phase difference based on all phase FFT (apFFT) were analyzed and compared with. To avoid the interference of circuit and sensors, the double homologous sine sending signals with different transmission distance was used. Theory and simulation results showed that, when signal frequency was known, the phase difference based on FFT had a good result. When signal frequency was 40 kHz, Signal Noise Ratio (SNR) was 25 dB, sampling points was 2048,A/D bits were 11 bits and the sampling rate was 200 kHz, the error of the measurement of transmission time was less than 10 ns. When signal frequency was unknown, the phase difference based on apFFT had a good result.