Geologic mapping in the northern Sierra Los Ajos reveals new stratigraphic and structural data relevant to deciphering the Mesozoic–Cenozoic tectonic evolution of the range. The northern Sierra Los Ajos is cored by Proterozoic, Cambrian, Devonian, Mississippian, and Pennsylvanian strata, equivalent respectively to the Pinal Schist, Bolsa Quartzite and Abrigo Limestone, Martin Formation, Escabrosa Limestone, and Horquilla Limestone. The Proterozoic–Paleozoic sequence is mantled by Upper Cretaceous rocks partly equivalent to the Fort Crittenden and Salero Formations in Arizona, and the Cabullona Group in Sonora, Mexico.

Absence of the Upper Jurassic–Lower Cretaceous Bisbee Group below the Upper Cretaceous rocks and above the Proterozoic–Paleozoic rocks indicates that the Sierra Los Ajos was part of the Cananea high, a topographic highland during the Late Jurassic and Early Cretaceous. Deposition of Upper Cretaceous rocks directly on Paleozoic and Proterozoic rocks indicates that the Sierra Los Ajos area had subsided as part of the Laramide Cabullona basin during Late Cretaceous time. Basal beds of the Upper Cretaceous sequence are clast-supported conglomerate composed locally of basement (Paleozoic) clasts. The conglomerate represents erosion of Paleozoic basement in the Sierra Los Ajos area coincident with development of the Cabullona basin.

The present-day Sierra Los Ajos reaches elevations of greater than 2600 m, and was uplifted during Tertiary basin-and-range extension. Upper Cretaceous rocks are exposed at higher elevations in the northern Sierra Los Ajos and represent an uplifted part of the inverted Cabullona basin. Tertiary uplift of the Sierra Los Ajos was largely accommodated by vertical movement along the north-to-northwest-striking Sierra Los Ajos fault zone flanking the west side of the range. This fault zone structurally controls the configuration of the headwaters of the San Pedro River basin, an important bi-national water resource in the US-Mexico border region.