In this study, a matched-mode autoregressive source depth estimation method (MMAR) based on autoregressive (AR) wavenumber estimation is proposed for a moving source in shallow water waveguides. The signal original frequency and the environmental parameters, namely, the sound speed profile and bottom properties are known as a prior knowledge. The mode wavenumbers are estimated by the AR modal wavenumber spectrum. On the basis of the mode wavenumber estimation, the mode amplitudes can be estimated by the wavenumber spectrum that is obtained by generalized Hankel transform. The source depth estimation is determined by the peak of source depth function wherein the data mode best matches the replica mode that is calculated using a propagation model. Compared with other methods of moving source depth estimation, the proposed method exhibits a better performance in source depth estimation under low signal-to-noise ratio or the small range span. The selection of horizontal line array depth is illustrated by simulation and normal mode theory in details.