Recently, kagome lattice materials have emerged as a new model material platform for discovering and engineering novel quantum phases of matter. In this work, we elucidate the driving mechanism of the 3 × 3 charge order in a newly discovered kagome metal ScV6Sn6. Through multimodal investigations combining angle-resolved photoemission spectroscopy, phonon dispersion calculations, and phase diagram study, we identify the central role of unstable planar Sn and Sc phonon modes, while the electronic instability and van Hove singularities originating from the V kagome lattice have a marginal influence. Our results highlight that the 3 × 3 charge order in ScV6Sn6 is fundamentally distinguished from the electronically driven 2 × 2 charge order in the canonical kagome system AV3Sb5, uncovering a new mechanism to induce symmetry-breaking phase transition in kagome lattice materials.