The stratigraphy of the Sanqing Mountain area is relatively complete. In the park and surrounding areas, strata from the Neoproterozoic to the Quaternary are all exposed, recording the geological evolution history and significant geological events of the region since the Neoproterozoic. 

In the Neoproterozoic, the Nanhua System consists of marine clastic rocks and glacial tillite interbedded with limestone; the Sinian System consists of siliceous rocks and carbonate rocks; they are distributed in the cores of the complex anticlines within the park.

In the Paleozoic, the Cambrian and Ordovician systems are mainly distributed around Sanqing Mountain, while the Silurian to Upper Paleozoic have been mostly eroded within the park but can be seen in the surrounding areas outside the park. Specifically: the Cambrian is dominated by carbonate rocks interbedded with mudstone and siliceous shale, with black shale at the bottom and sponge spicules produced; the Ordovician mainly consists of shale interbedded with nodular limestone, with abundant graptolite fossils in the regional strata; the Silurian consists of muddy and sandy clastic rocks; the Devonian includes conglomerates, quartz sandstones, and silty shales, often unconformably overlying the pre-Devonian strata; the Carboniferous and Permian are mainly composed of carbonate rocks.

No Mesozoic strata are found within the park; these strata are mainly found in terrestrial faulted basin areas outside the park. However, five rock suites of Early Cretaceous intrusive rocks are present within the park, forming part of the Mesozoic Huaiyushan granite massif (Huaiyushan sequence).

In the Cenozoic, only the Quaternary is developed, including the Pleistocene and Holocene. Its distribution is limited, mainly found in valleys and plains, primarily consisting of alluvial clay, silty clay, sand and gravel layers, or residual colluvial clay with cobbles.