High-dimensional quantum systems, such as qutrits (quantum three-level systems), have multiple accessible energy levels beyond the two-level qubits. Therefore, qutrits can offer a larger state space to improve the efficiency of quantum computation. Here, we demonstrate a high-fidelity iSWAP-like gate operation on a frequency-tunable superconducting qutrits system. The superconducting quantum system consists of two qutrits that are coupled via a resonator with fixed qutrit-resonator coupling strengths. Through designing the frequency pulse profile and optimizing the parameter values, the gate error can be suppressed below 1.5 × 10−3. To bear out the feasibility of the proposal, we have conducted our study with experimentally accessible parameters. As the resonator can mediate the interaction between the irrelevant qutrits, the presented approach can also be used to couple multiple qutrits together, providing a good platform for quantum information processing.