Exploring ultrafast magnetization control in 2D magnets via laser pulses is established, yet the interplay between spin dynamics and the lattice remains underexplored. Utilizing real-time time-dependent density functional theory (rt-TDDFT) coupled with Ehrenfest dynamics and nonadiabatic molecular dynamics (NAMD) simulations, we systematically investigate the laser-induced spin-nuclei dynamics with pre-excited A1g and E2g coherent phonons in the 2D ferromagnet Fe3GeTe2 (FGT) monolayer. Selective pre-excitation of coherent phonons under ultrafast laser irradiation significantly alters the local spin moment of FGT, consequently inducing additional spin loss attributed to the nuclear motion-induced asymmetric interatomic charge transfer. Excited spin-resolved charge undergoes a bidirectional spin-flip between spin-down and spin-up states, characterized by a subtle change in the spin moment within approximately 100 fs, followed by unidirectional spin-flip, which will further contribute to the spin moment loss of FGT within tens of picoseconds. Our results shed light on the coupling of coherent phonons with magnetization dynamics in 2D limit.