The tectonic evolution of the Central Asian Orogenic Belt (CAOB) is characterized by the successive accretion of lithospheric blocks, leading to different interpretations about the polarity of subductions during the Paleozoic, the number of microplates and oceanic basins and the timing of tectonic events. This is especially the case in the Tien Shan area. In this paper, we propose new structural maps and cross-sections of Middle and South Kyrgyz Tien Shan (MTS and STS respectively). These cross-sections highlight an overall dextral strike-slip shear zone in the MTS at the crustal scale and a North verging structure in the STS. These structures are Carboniferous in age and sealed by a late Carboniferous conglomerate, later overlain by Mesozoic and Cenozoic deposits. The STS exhibits two deformation phases: (1) a top-to-the-South normal shearing that can be related to subduction or exhumation dynamics and (2) a top to the North nappe stacking that we link to the late Paleozoic collisional events between the MTS and the Tarim block. We propose a new interpretation of the tectonic evolution of the Kyrgyz Tien Shan during the Late Paleozoic collision. This model involves a partitioned collisional deformation in Late Carboniferous times, with an orthogonal collision to the south, between the Tarim and MTS, and a strike-slip regime to the north along a dextral E-W zone located between the MTS and the North Tien-Shan/ Kazakh platform, the so-called Nikolaev Line. The docking of the large Tarim Craton against the CAOB corresponds to a collision phase, which ended the long-lived Paleozoic subduction history in the CAOB and was followed in the TS region by intense strike-slip deformation during the Permian.