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Abstract Quantum key distribution (QKD) can share an unconditional secure key between two remote parties, but the deviation between theory and practice will break the security of the generated key. In this paper, we evaluate the security of QKD with weak basis-choice flaws, in which the random bits used by Alice and Bob are weakly controlled by Eve. Based on the definition of Li et al. (Sci Rep 5:16200, 2015) and GLLP’s analysis, we obtain a tight and analytical bound to estimate the phase error and key rate for both the single photon source and the weak coherent source. Our approach largely increases the key rate from that of the original approach. Finally, we investigate and confirm the security of BB84-QKD with a practical commercial devices.