Shoushan was formed by sedimentation about 1.8 million years ago as part of the Kutingkeng Formation: badland terrain formed by dark grey mudstones interspersed with fine to medium grain sandstones, easily liquefy when in contact with water. About 1.25 million years ago, the area of the present day Shoushan was once a shallow water region, abundant with coral, algae, foraminifers and seashell growths. The remains of these organisms formed the hard limestone known as the “Kaohsiung Limestone” today, which was layered on top of the Kutingkeng formation and formed the basis of Shoushan Mountain. Erosion from latter periods resulted in large sedimentations that hindered the growths of corals, and terminated the formation of coral reefs. The Chijou layer was then formed with sand stones and mud stones. The rock layer was squeezed, uplifted, folded, fractured and jointed. The Kaohsiung limestone collapsed and accumulated on the southeastern side of Shoushan, forming Shoushan limestone. After weathering, erosion and rainwater erosion, the softer and weaker rocks beside the limestone were washed away and exposed the limestone, resulting in the frequently seen reef rocks, caves, gorges and cliff terrains on the mountain. Prolonged corrosion of the terrain resulted in the many limestone caves on the mountain, which are abundant with magnificent displays of stalactites, stalagmites and stone pillars, formed by precipitations of calcium carbonate.

Banpingshan is a single-sided, slanted mountain. There are cliffs on the west side of the ridgeline, covered mostly in collapsed limestone, while few areas are exposed mudstone (Kutingkeng) layers. The east side of the ridgeline has limestone layers, with growing thickness from north to south. A major characteristic of the development of coral reefs on Banpingshan is the large mixture of muddy detritus in the coral reef layer, forming interlacing layers of shallow water limestone and large amount of silicate detritus mud layers, which are significantly different from the common coral reefs formed on hard substrates (like the limestone in Hengchun).

Gueishan is situated within the Old City of the Zuoying District and faces Banpingshan. Originally, a coral reef limestone under the ocean, the mountain was raised as the result of tectonic uplift. Its geological structure is similar to both Shoushan and Banpingshan. Qihou Mountain belongs to the Kaohsiung limestone stratum that was formed from ancient coral reefs, with sand layers and clay layers interspersing the rock layers. Fossilized corals can be found frequently on the limestone and are evidence of an uplifted ocean floor.