/ AbstractCharge density waves (CDWs) have been tied to a number of unusual phenomena in kagome metals, including rotation symmetry breaking, time-reversal symmetry breaking and superconductivity. The majority of the experiments thus far have focused on the CDW states in AV3Sb5 and FeGe, characterized by the 2a0 by 2a0 period. Recently, a bulk CDW phase (T* ~ 92 K) with a different wave length and orientation has been reported in ScV6Sn6, as the first realization of a CDW state in the broad RM6X6 structure. Here, using a combination of scanning tunneling microscopy/spectroscopy and angle-resolved photoemission spectroscopy, we reveal the microscopic structure and the spectroscopic signatures of this charge ordering phase in ScV6Sn6. Differential conductance dI/dV spectra show a partial gap opening in the density-of-states of about 20 meV at the Fermi level. This is much smaller than the spectral gaps observed in AV3Sb5 and FeGe despite the comparable T* temperatures in these systems, suggesting substantially weaker coupling strength in ScV6Sn6. Surprisingly, despite the three-dimensional bulk nature of the charge order, we find that the charge modulation is only observed on the kagome termination. Temperature-dependent band structure evolution suggests a modulation of the surface states as a consequence of the emergent charge order, with an abrupt spectral weight shift below T* consistent with the first-order phase transition. The similarity of the electronic band structures of ScV6Sn6 and TbV6Sn6 (where charge ordering is absent), together with the first-principle calculations, suggests that charge ordering in ScV6Sn6 may not be primarily electronically driven. Interestingly, in contrast to the CDW state of cousin AV3Sb5, we find no evidence supporting rotation symmetry breaking. Our results reveal a distinctive nature of the charge ordering phase in ScV6Sn6 in comparison to other kagome metals.