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 Δ 1CO ≈ 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 Δ 1CO, 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.