In this work, a novel method is put forward to quantitatively simulate the subsurface damages microstructural alteration of titanium alloy components subjected to microscale cutting. A trans-scale numerical framework is conducted with the purpose of revealing the underlying influence mechanism of tool structure parameters on subsurface dislocation configurations using a dislocation dynamics-based model, which considers both dislocation structural transformation and grain refining. Results showed that the developed framework not only captured the essential features of workpiece microstructure, but also predicted the subsurface damages layer states and their modifications. A series of defects were found in the material subsurface during the orthogonal cutting of titanium alloy, such as edge and screw dislocations, junctions, parallel slip lines, intersection dislocation bands, vacancy defects, and refinement grains. Particularly, in the process of micro-cutting, the depth of subsurface damages layer increased significantly with cutting length at the beginning, and then remained unchanged in the stable removal phase. Moreover, smaller edge radius and larger rake angle can greatly weaken the squeezing action and heat diffusion effect between the tool tip and workpiece, which further prevents the formation of subsurface defects and enhances finished surface quality. In addition, although increasing tool clearance angle could drastically lighten the thickness of subsurface damages layer, it is noteworthy that its performance would be decreased significantly when the clearance angle was greater than or equal to 5°. The micro-end-milling experiment was performed to validate the existing simulation results, and the results show very good agreement.