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Abstract To achieve universal quantum computation via general fault-tolerant schemes, stabilizer operations must be supplemented with other non-stabilizer quantum resources. Motivated by this necessity, we develop a resource theory for magic quantum channels to characterize and quantify the quantum ‘magic’ or non-stabilizerness of noisy quantum circuits. For qudit quantum computing with odd dimensiond, it is known that quantum states with non-negative Wigner function can be efficiently simulated classically. First, inspired by this observation, we introduce a resource theory based on completely positive-Wigner-preserving quantum operations as free operations, and we show that they can be efficiently simulated via a classical algorithm. Second, we introduce two efficiently computable magic measures for quantum channels, called the mana and thauma of a quantum channel. As applications, we show that these measures not only provide fundamental limits on the distillable magic of quantum channels, but they also lead to lower bounds for the task of synthesizing non-Clifford gates. Third, we propose a classical algorithm for simulating noisy quantum circuits, whose sample complexity can be quantified by the mana of a quantum channel. We further show that this algorithm can outperform another approach for simulating noisy quantum circuits, based on channel robustness. Finally, we explore the threshold of non-stabilizerness for basic quantum circuits under depolarizing noise.