Cobalt-rich manganese crusts (CRCs) are important as a potential mineral source that could occur throughout the Pacific on seamounts, ridges, and plateaus. We built a prototype parametric acoustic probe to complete the task of in-situ thickness measurements to estimate the volumetric distribution of deep-sea mineral. The prototype is designed with dual-channels for receiving the primary and secondary signal, which lays a foundation for improving the thickness extraction algorithm. Considering that the signal quality is degraded by the system interference and ambient noise, some improvements to the algorithm are proposed by including the wavelet-based envelope extraction method and the adaptive estimation strategy based on the dual-channel information. Additionally, wavelet regression is applied to reduce the measuring noise assuming that the CRCs have local thickness invariability. The algorithm is suitable for the CRCs with the structure of the multilayers at the top surface and one single layer at the bottom surface. A laboratory experiment is performed to validate the effectiveness of the algorithm. The experiments carried out on the China Ocean 51th voyage in the Western Pacific Ocean on Aug 30, 2018, are described and the data obtained by using the sit-on-bottom stationary measurement are processed to validate the design of the prototype.