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The mechanisms of nickel thin films irradiated by femtosecond laser pulse trains are studied by a model using molecular dynamics simulations and two-temperature model. It is found that the pulse train technology can change energy transport and corresponding phase change processes. Compared with single pulse ablation at the same total fluence, the pulse trains lead to (1) lower ablation rate with more and smaller uniform nanoparticles, (2) higher film surface temperatures and longer thermalization time, (3) much lower electron thermal conductivity that can further control heat-affected zone, (4) significantly smaller film compressive stresses and tensile stresses which reduce microcracks, and (5) a transition from phase explosion to the critical point phase separation which favors small uniform nanoparticle generation.