Qutrit entanglement and joint multi-parameter estimation in an optical clock platform

Quantum metrology harnesses entanglement to improve measurement precision beyond classical limits. While standard protocols rely on two-level qubits to estimate a single parameter, extending them to entangled multi-level qudits enables the optimal simultaneous estimation of multiple parameters within a single probe. However, generating such multi-level entanglement and harnessing it for joint multi-parameter estimation in atomic clocks has remained an outstanding challenge. Here, we experimentally demonstrate genuine qutrit entanglement and joint multi-parameter estimation in an optical clock platform. Leveraging control over the ground state and two fine-structure clock states of $^{88}\text{Sr}$ atoms trapped in triple-magic optical tweezers, we generate a maximally entangled two-qutrit state with a loss-postselected fidelity of F = 0.85(1), certifying genuine multi-level entanglement. Taking advantage of this high-dimensional entanglement, we theoretically construct and experimentally realize an optimal two-qutrit metrological probe state and noise-robust readout circuit to simultaneously estimate injected phases on two optical clock transitions. We observe a joint estimation variance below the ideal individual two-level sensing threshold, and show theoretically that this advantage persists at state-of-the-art atom numbers under circuit-level noise. These results demonstrate the key building blocks towards quantum information science with high-dimensional states encoded in the internal energy levels of neutral atoms.