Considering fluctuant dark count rate in practical quantum key distribution (QKD) system, a new decoy-state method with one vacuum state and one weak decoy state is presented based on a heralded single photon source (HSPS). The method assumes that the dark count rate of each pulse is random and independent. The lower bound of the count rate and the upper bound of the error rate of a single photon state are estimated. The method is applied to the decoy-state QKD system with and without the fluctuation of dark count rate. Because the estimation of the upper bound of a single photon state’s error rate is stricter, the method can obtain better performance than the existing methods under the same condition of implementation.