Charge density waves (CDWs) in kagome metals have been tied to many exotic phenomena. Here, using spectroscopic-imaging scanning tunneling microscopy and angle-resolved photoemission spectroscopy, we study the charge order in kagome metal ScV₆Sn₆. The similarity of electronic band structures of ScV₆Sn₆ and TbV₆Sn₆ (where charge ordering is absent) suggests that charge ordering in ScV₆Sn₆ is unlikely to be primarily driven by Fermi surface nesting of the Van Hove singularities. In contrast to the CDW state of cousin kagome metals, we find no evidence supporting rotation symmetry breaking. Differential conductance dI/dV spectra show a partial gap Δ¹_CO ≈ 20 meV at the Fermi level. Interestingly, dI/dV maps reveal that charge modulations exhibit an abrupt phase shift as a function of energy at energy much higher than Δ¹_CO, which we attribute to another spectral gap. Our experiments reveal a distinctive nature of the charge order in ScV₆Sn₆ with fundamental differences compared to other kagome metals.