There is a cross-cutting relationship between the E-W trending structures and the NE-trending structures in the northern Longmen-Micang Mountains region, which reflects possible regional tectonic transition and migration. Apatite fission track (AFT) analyses of 15 samples collected from this area yield apparent ages varying from 30.3±4.2 Ma to 111.7±9.0 Ma and confined-track-lengths ranging from 10.6±0.3 μm to 12.4±0.1 μm. Four specific groups were identified on the basis of the Track Age Spectrum Calculation (TASC) patterns, i.e., 143–112?Ma, 93.6–88?Ma, 42–40?Ma and ~25.6?Ma. These age groups correspond to the spatial distributions of datasets and may represent four tectonic events. Together with the regional deformation patterns, the four age groups are interpreted to indicate tectonic superposition, transition and migration during the Meso-Cenozoic with the following possible order: (1) the Micang Mountains belt was dominated by the E-W trending structure during 143–112?Ma; (2) the contraction of the Longmen Mountains belt from the NW to the SE during 93.6–88?Ma led to the superposition of the NE-trending structures over the E-W trendinding structures; (3) dextral strike-slip shear dominated the Longmen Mountains belt at 42–40?Ma; (4) westward migration of the active tectonic belt occurred from 93.6–25.6?Ma in a break-back sequence in the northern Longmen Mountains belt. The Late Cenozoic tectonics in the northern Longmen Mountains belt are characterized by the dextral strike-slip shear and the occurrence of westward break-back sequence of deformations. As a result, north-south differences in deformations along the Longmen Mountains belt were intensified since the Miocene time and strains were mainly accumulated in the hinterland of the Longmen Mountains instead of being propagated to the foreland basin.