Acoustic pyrometry is a non-contact measurement technology for monitoring furnace combustion reaction, diagnosing energy loss due to incomplete combustion and ensuring safe production. The accuracy of time of flight (TOF) estimation of an acoustic pyrometry directly affects the authenticity of furnace temperature measurement. In this paper presented is a novel TOF (i.e. time delay) estimation algorithm based on digital lock-in filtering (DLF) algorithm. In this research, the time-frequency relationship between the first harmonic of the acoustic signal and the moment of characteristic frequency applied is established through the digital lock-in and low-pass filtering techniques. The accurate estimation of TOF is obtained by extracting and comparing the temporal relationship of the characteristic frequency occurrence between received and source acoustic signals. The computational error analysis indicates that the accuracy of the proposed algorithm is better than that of the classical generalized cross-correlation (GCC) algorithm, and the computational effort is significantly reduced to half of that the GCC can offer. It can be confirmed that with this method, the temperature measurement in furnaces can be improved in terms of computational effort and accuracy, which are vital parameters in furnace combustion control. It provides a new idea of time delay estimation with the utilization of acoustic pyrometry for furnace.