The discrepancy between theory and experiment severely limits the development of quantum key distribution (QKD). Reference-frame-independent (RFI) protocol has been proposed to avoid alignment of the reference frame. However, multiple optical modes caused by Trojan horse attacks and equipment loopholes lead to the imperfect emitted signal unavoidably. In this paper, we analyzed the security of the RFI-QKD protocol with non-qubit sources based on generalizing loss-tolerant techniques. The simulation results show that our work can effectively defend against non-qubit sources including a misaligned reference frame, state preparation flaws, multiple optical modes, and Trojan horse attacks. Moreover, it only requires the preparation of four quantum states, which reduces the complexity of the experiment in the future.
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