In the southwestern Sichuan Basin, the Jurassic Shaximiao Formation encompasses a multitude of working areas, displaying intricate sedimentary traits. Traditional methods of stratigraphic division based on sequence suffer from inherent subjectivity and limitations. This study employs a combined mathematical approach to use the wavelet transform (WT) and the Hilbert–Huang transform (HHT). It decomposes the natural gamma ray (GR) logging curve into energy spectrum plots and wavelet coefficients at different scales, high and low frequency signals at different frequencies, and a set of intrinsic mode function components and residual functions. The study conducted a detailed stratigraphic division of the Jurassic Shaximiao Formation in the southwestern Sichuan Basin using these methods. The WT offers greater resolution for the periodic changes in the base level, whereas the HHT demonstrates a superior correlation with the positions of stratigraphic interfaces. The combined utilization of the continuous wavelet transform, the discrete wavelet transform, and HHT methods has demonstrated encouraging outcomes in the stratigraphic division of the Jurassic Shaximiao Formation. These methods have been shown to enhance the accuracy of stratigraphic division and to reduce the influence of subjective factors. This study presents new insights and approaches for geological data processing, offering significant theoretical and practical implications and novel technical means for oil and gas exploration and development.