In this paper, we propose an threshold-based Schur algorithm for estimating the media characteristics of sub-bottom multi-layers by using the signal generated by a parametric array transducer. We use the KZK model to generate a parametric array signal, and use the proposed threshold-based Schur algorithm for estimating the reflection coefficients of multiple sea bottom layers. Using computer simulation, we verify that the difference frequency component generated by the KZK model prevails over the signals of primary frequencies at long range. For the simulation, we use the transmit signal generated by the KZK and the reflected signal obtained from a lattice filter model for the seawater and sub-bottom of multi-level non-homogeneous layers. Through the simulation, we verify that the proposed threshold-based Schur algorithm can give much more accurate and efficient estimates of the reflection coefficients than methods using received signal, matched filter output signal, and normal Schur algorithm output.