Kagome lattice materials offer a fertile ground to discover novel quantum phases of matter, ranging from unconventional superconductivity and quantum spin liquids to charge orders of various profiles. However, understanding the genuine origin of the quantum phases in kagome materials is often challenging, owing to the intertwined atomic, electronic, and structural degrees of freedom. Here, we combine angle-resolved photoemission spectroscopy, phonon mode calculation, and chemical doping to elucidate the driving mechanism of the √3×√3 charge order in a newly discovered kagome metal ScV₆Sn₆. In contrast to the case of the archetype kagome system AV₃Sb₅ (A= K, Rb, Cs), the van Hove singularities in ScV₆Sn₆ remain intact across the charge order transition, indicating a marginal role of the electronic instability from the V kagome lattice. Instead, we identified a three-dimensional band with dominant planar Sn character opening a large charge order gap of 260 meV and strongly reconstructing the Fermi surface. Our complementary phonon dispersion calculations further emphasize the role of the structural components other than the V kagome lattice by revealing the unstable planar Sn and Sc phonon modes associated to the √3×√3 phase. Finally, in the constructed phase diagram of Sc(V_1-xCr_x)₆Sn₆, the charge order remains robust in a wide doping range x ≈ 0 ~ 0.10 against the Fermi level shift up to ≈ 120 meV, further making the electronic scenarios such as Fermi surface or saddle point nesting unlikely. Our multimodal investigations demonstrate that the physics of ScV₆Sn₆ is fundamentally different from the canonical kagome metal AV₃Sb₅, uncovering a new mechanism to induce symmetry-breaking phase transition in kagome lattice materials.