Abstract: Aiming at the problem of inaccurate time of arrival (TOA) extraction caused by low signal-to-noise ratio (SNR) of received signals in wide area multilateration system, a joint TOA estimation algorithm combining matched filter and non-coherent integration is proposed, which can effectively reduce the root mean square error (RMSE) of the matched filter TOA estimation method under low SNR. The joint algorithm does the non-coherent integration of the matched filter output of the received reply signals within the dwell time of the secondary surveillance radar, marks a time stamp at the maximum point for TOA estimation, and uses the principle of energy accumulation to improve the SNR, so as to improve the estimation accuracy. The simulation results show that the algorithm can achieve a TOA estimation accuracy of 24.302 ns at −15 dB SNR, 53 MHz sampling frequency and 9 accumulated signals. The proposed joint TOA estimation algorithm has the characteristics of high accuracy and high robustness, and can improve the estimation accuracy to less than 25 ns at the SNR of −15 dB to 0 dB. It provides an effective method for extracting the TOA of mode S signals with low SNR and improving the positioning accuracy of wide area multilateration.