Noise is a major challenge for building practical quantum computing systems. Precise characterization of quantum noise is crucial for developing effective error mitigation and correction schemes. However, state preparation and measurement (SPAM) errors on many current platforms can introduce large ambiguity into conventional noise characterization methods. In this work, we propose a scheme for enhancing quantum noise characterization using additional energy levels. We first develop a comprehensive theory on the identifiability of n-qudit SPAM noise given high-quality single-qudit control, showing the existence of gauge freedoms which can be completely described using subsystem depolarizing maps. We then show how to use these extra energy levels to reduce the gauge ambiguity in characterizing both SPAM and gate noise in the qubit subspace. We experimentally implement these ideas on a superconducting quantum computing device and demonstrate a qutrit-enabled enhancement in noise characterization precision.

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