Mixed deposition in shallow seas is highly sensitive to climate variations and sea-level changes, which are the primary controls of high-frequency cycles in the stratigraphic record. The widespread Lower Permian mixed carbonate-siliciclastic succession of the Paraná Basin is composed of rhythmic organic-rich shale interbedded with dolostone. The strata are organized into several orders of magnitude of superimposed asymmetrical and symmetrical facies stacking patterns that developed in a broad epeiric sea, which extended over 106 km2 of Permian Gondwanan land. Detailed sedimentological and stratal stacking analysis allow the hierarchical organization to be identified in large-scale, medium-scale, small-scale, and elementary stacking patterns. The high-frequency depositional cycles compose four 3rd-order sequences. They comprise gray to black shale, marls, and peloidal to micritic dolostone. Due to the shallow water setting, the minimal available accommodation is responsible for the reduced cycle thickness and the overall mixed succession. The rhythmic deposits host highly productive hydrocarbon source rocks. Two widespread, thicker intervals of bituminous shale that develop during 3rd-order sequence transgression events are highly organic-rich oil shale (27 wt%). In addition, thin black shale laminae, which are interbedded with dolostone in high-frequency stacking patterns, are also rich in organic carbon (2–8 wt%). The alternation of high carbonate content and organic matter production was controlled by wet‒dry seasons and was related to total solar radiation maxima and minima. The total solar radiation maxima are translated into elevated carbonate precipitation due to shallower and hypersaline conditions. Total solar radiation minima induce freshwater discharge in shallow and hypersaline environments during wet stages, resulting in water column stratification. The occurrence of kerogen types III and IV, a high gammacerane index, variable Pr/Ph ratios, and C35 homohopane indices indicate this condition. In addition, the input of nutrient-rich terrigenous sediments favor algal blooms, enhancing anoxia in the bottom water, which is responsible for the organic-rich shale facies, as indicated by kerogen types I and II, high hydrogen index values, high C27/C29 sterane ratios, and higher β-carotane values. Based on the hierarchical organization and previous U–Pb SHRIMP zircon ages of volcanic ash layers, it is possible to correlate the observed succession with the global sea-level curve. A time span of 8.0 Ma is assessed for the Irati Sea, with an average of 2.7 Ma for the large-scale cycles. Furthermore, the high-frequency patterns that are compatible with the precession and eccentricity of the short (±100 ka) and major (±400 ka) periodicities of the Earth's orbit are estimated to be 26.6 ka, 135.5 ka, and 400 ka. The high-frequency cycles of organic-rich shales and carbonate that are deposited over thousands of years under long-term sea-level changes and are correlated along the basin suggest climatic control driven by the Earth's orbital perturbation, which is possible in the Milankovitch frequency band.