The Mahu Sag, a crucial hydrocarbon-bearing depression in the Junggar Basin, has recently been identified as having significant oil reservoirs within the deep layers of the Lower Wuerhe Formation (Middle Permian). However, the lack of a unified high-frequency sequence stratigraphic framework for this formation has impeded isochronous sand body correlation and hindered sustainable hydrocarbon exploration. In this study, we integrate traditional sequence stratigraphy with astronomical cycle theory by utilizing spectral analysis and correlation coefficient (COCO) analysis on natural gamma-ray logging curves. Our results indicate that sedimentation of the Lower Wuerhe Formation was significantly controlled by astronomical cycles. Spectral analysis reveals that the deposition time of three third-order sequences ranges from 0.83 to 2.06 million years. Combined with seismic profiles and Integrated Prediction Error Filter Analysis (INPEFA) technology, we further identify the superimposed cyclic characteristics of the strata. Through multi-scale analysis, the Lower Wuerhe Formation is subdivided into three third-order sequences, eleven fourth-order sequences, and twenty-six fifth-order sequences. This research establishes a multi-level isochronous stratigraphic framework for the Lower Wuerhe Formation, enhancing the precision and efficiency of hydrocarbon exploration and supporting more sustainable energy development.