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Improving the qubit’s lifetime (T1) is crucial for fault-tolerant quantum computing. Recent advancements have shown that replacing niobium (Nb) with tantalum (Ta) as the base metal significantly increases T1, likely due to a less lossy native surface oxide. However, understanding the formation mechanism and nature of both surface oxides is still limited. Using aberration-corrected transmission electron microscopy and electron energy loss spectroscopy, we found that Ta surface oxide has fewer suboxides than Nb oxide. We observed an abrupt oxidation state transition from Ta2O5to Ta, as opposed to the gradual shift from Nb2O5, NbO2, and NbO to Nb, consistent with thermodynamic modeling. Additionally, amorphous Ta2O5exhibits a closer-to-crystalline bonding nature than Nb2O5, potentially hindering H atomic diffusion toward the oxide/metal interface. Finally, we propose a loss mechanism arising from the transition between two states within the distorted octahedron in an amorphous structure, potentially causing two-level system loss. Our findings offer a deeper understanding of the differences between native amorphous Ta and Nb oxides, providing valuable insights for advancing superconducting qubits through surface oxide engineering.