The Liangshan and Qixia formations in the Sichuan Basin of central China were formed in the earlier middle Permian. Based on outcrop observation of the Changjianggou section at Shangsi, Guangyuan region and 3rd-order sequence division in typical drillings, one-dimensional spectrum analysis has been used to choose the better curve between the natural gamma ray spectrometry log(ln(Th/K)) in Well-Long17 and the gamma ray log(GR) in Well-Wujia1, respectively, for identifying Milankovitch cycles in Sequence PSQ1 which comprises the Liangshan and Qixia formations, and then to identify the variation in the Milankovitch cycle sequences. On this basis, the system tract and 4th-order sequence interfaces in Sequence PSQ1 were found via two-dimensional spectral analysis and digital filtering. Finally, a high-frequency sequence division program was established. Among these cycles, long eccentricity (413.0 ka) and short eccentricity (123.0 ka) are the most unambiguous, and they are separately the major control factors in forming 4th-order (parasequence sets) and 5th-order (parasequences) sequences, with the average thicknesses corresponding to the main cycles being 11.47 m and 3.32 m in Well-Long17, and 14.21 m and 3.79 m in Well-Wujia1, respectively. In other words, the deposition rate in the beach subfacies is faster than that of the inner ramp facies. The ln(Th/K) curve is more sensitive than the GR as the index of relatively ancient water depth in carbonate deposition. One-dimensional spectrum analysis of ln(Th/K) curve could distinguish the Milankovitch cycle sequences that arose from the Precession cycle (20.90 ka), with a much higher credibility. Sequence PSQ1 in Well-Long17 contains 10 4th-order sequences, and the growth span of Sequence PSQ1 consisting of the Liangshan and Qixia formations is about 4.13 Ma. The single deposition thickness of the long eccentricity cycle sequence has the characteristics of thinning and then thickening in the two-dimensional spectrum, which could be used to identify the system tract interface of the 3rd-order sequence. The precession sequence thickness remains stationary. As a result, the early deposition rate in the mid-Permian of the Sichuan basin was very slow, remaining nearly stationary, and this reflects a sustained depositional environment. Whole-rock carbon and oxygen isotope curves could also prove this point. Milankovitch cycle sequence studies provide a basis for paleoenvironmental analysis and, as such, can be used to analyze ancient climate change, calculate deposition rate and deposition time, and carry out fine isochronous stratigraphic correlation.