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In this paper, we proposed the scheme for a passive round-robin differential-phase-shift quantum key distribution (RRDPS-QKD) set-up based on the principle of Hong–Ou–Mandel interference. Our scheme requires two legitimate parties to prepare their signal state with two different non-orthogonal bases instead of single in original protocol. Incorporating this characteristic, we establish the level of security of our protocol under the intercept-resend attack and demonstrate its detector-flaw-immune feature. Furthermore, we show that our scheme not only inherits the merit of better tolerance of bit errors and finite-sized-key effects but can be implemented using hardware similar to the measurement device independent QKD (MDI-QKD). This ensures good compatibility with the current commonly used quantum system.