We utilize near-infrared femtosecond pulses to investigate coherent phonon oscillations of Ca2RuO4. The coherent Ag phonon mode of the lowest frequency changes abruptly not only its amplitude but also the oscillation phase as the spin order develops. In addition, the phonon mode shows a redshift entering the magnetically ordered state, which indicates a spin-phonon coupling in the system. Density functional theory calculations reveal that the Ag oscillations result in octahedral tilting distortions, which are exactly in sync with the lattice deformation driven by the magnetic ordering. We suggest that the structural distortions by the spin-phonon coupling can induce the unusual oscillation phase shift between impulsive and displacive type oscillations. © 2019 American Physical Society.