Soil thickness is an important parameter affecting soil quality. Rapid acquisition of accurate soil thickness information is an important data basis for the analysis and evaluation of the quality of cultivated land resources and its changing trend. Current mainstream measurement methods are inefficient or inaccurate, such as radar detection method and borehole sampling method. The rapid measurement of soil thickness was realized based on soil mechanical resistance with optimized cone meter. Data were acquired by a cone soil thickness measuring instrument which was an optimized handheld cone meter attached with acceleration sensor, position sensor and other sensors. Acceleration compensation technology was adopted to reduce the measurement error of soil mechanical resistance caused by nonuniform speed penetration of cone meter. Envelope detection and Hilbert instantaneous amplitude eigenvalue clustering algorithm were introduced to identify soil structure and calculate the thickness of soil layer. The simulation results based on Ayers semiempirical model showed that the conical soil thickness measuring instrument based on Hilbert transform algorithm can effectively acquire the information of soil thickness with relative error no higher than 7.50%. The measuring results for outdoor measured data showed that the absolute error of soil thickness measured by Hilbert instantaneous amplitude spectrum based on lower envelope was not more than 1cm, and the relative error was not more than 10%. This method can meet the needs of actual measurement for plough layer soil depth and provide a reference for future soil layer measuring application.