The acoustic pyrometer system uses physical properties of the gas and registers the perceivable temperature without the effects of radiation, and the measuring accuracy of acoustic wave flight time is the major factor in its application. The traditional correlation algorithm could not overcome convolution interference and calculate the time delay of acoustic signals accurately, under the low SNR (Signal Noise Ratio) and complex reverberation noise conditions. This paper presents a generalized cross power spectrum algorithm to filter the product and convolution interferences, and improves the performances of anti-noise and anti-convolution by whitening the sample signals and adjusting the weighted value of cross power spectrum algorithm with the variation of SNR. The experimental result and theoretical analysis showed that the new generalized cross power spectrum algorithm compared to the traditional correlation function analytical algorithm, can overcome the convolution interferences from reverberation noise, and sharpen peak value, thereby estimate the time delays of signals accurately.