The geology of Kyrgyzstan is dominated by the complex sequences that comprise the Tien Shan mountain belt, itself forming the southwestern part of the much larger Urals-Mongolian fold belt. The mountains form an arc running through the country from west to east, with sub-parallel ranges separated by intermountain basins and valleys. The Ferganskiy Range in south-central Kyrgyzstan runs more in a northwest-southeasterly direction, and marks the divide between the principal tectonic blocks that are separated by a major regional fault, the Nikolaev Lineament. This effectively divides the Tien Shan into two; to the north the Northern Tien Shan is made up of folded Caledonian sequences, while south of the lineament lie younger Hercynian rocks. This area of the country can be further subdivided into the Central and Southern Tien Shan on account of their differing histories of formation.

The region identified today by the Tien Shan Mountains lies in a zone in which crustal movements have taken place since the Archaean. In consequence, it contains a wide variety of igneous, sedimentary and metamorphic rocks, formed at different periods under different geodynamic conditions. The mechanism of fold belt formation varied from time to time, with the northern section showing clear signs of polycyclic fold development, in which the Caledonian cycle was predominant, while in the Central Tien Shan, Hercynian-age structures dominate in a two-stage process. Further to the far south and west, single-stage Hercynian folding took place in rocks associated with the palaeo-Tethis Ocean, while those to the north originated in the Asian palaeo-ocean.

A clear distinction can also be drawn between the intensely complex pre-Mesozoic rocks, which form the core of the modern Tien Shan mountains, and later Mesozoic-Cainozoic rocks, mainly of continental sedimentary origin, that fill the basins between the mountain ranges. Carboniferous and Permian-age sediments and basalts thus occupy parts of northern Kyrgyzstan.