We perform first-principles calculations and coherent laser-matter interaction analyses to investigate the laser-induced ultrafast spin flip on graphene nanoflakes (GNFs) with transition metal elements attached on the boundary [TM&GNFs (TM = Fe, Co, Ni)]. It is shown that the spin-flip process on TM&GNFs is highly influenced by the involved element species and the position attached to the nanoflakes. Furthermore, taking Ni&GNF as an example, the first-principles tensile test predicts that the variation of the C–Ni bond length plays an important role in the spin density distribution, especially for the low-lying magnetic states, and can therefore dominate the spin-flip processes. The fastest spin-flip scenario is achieved within 80 fs in a Ni&GNF structure under 10% tensile strain along the C–Ni bond. The local deformation modulation of spin flip provides the precursory guidance for further study of ultrafast magnetization control in GNFs, which could lead to potential applications in future integrated straintronic devices.