Inner Space Cavern lies within limestone and dolomite rocks of the Edwards Group formed during the Cretaceous period.

As water from the surface became ground water, carbon dioxide (CO2) was picked up from the atmosphere and from decaying organic matter, creating carbonic acid (H2CO3), which would react with and dissolve the limestone rocks creating voids.

There were several large openings to the caverns during the Ice Age, an evidence of several skeletons of prehistoric Ice-Age animals including a baby mammoth, giant sloth and the saber-toothed tiger[2][3] have been found in the cavern; many were trapped in the cavern after they fell through the opening, unable to escape, and others drowned in thick, quicksand-like mud at the bottom of watering holes.

Inner Space Cavern was discovered by the Texas Highway Department drilling team in the spring 1963 during the construction of an overpass for Interstate 35.

Apart from the main entrance, which was created by dynamite blasts, a vertical borehole, located in the Inner Cathedral Room, serves as an emergency entryway/exit and a means for ventilating the cavern.