Recently the performance of the quantum key distribution (QKD) is substantially improved by the decoy state method and the non-orthogonal encoding protocol, separately. In this paper, a practical non-orthogonal decoy state protocol with a heralded single photon source (HSPS) for QKD is presented. The protocol is based on 4 states with different intensities, i.e. one signal state and three decoy states. The signal state is for generating keys; the decoy states arc for detecting the eavesdropping and estimating the fraction of single-photon and two-photon pulses. We have discussed three cases of this protocol, i.e. the general case, the optimal case and the special case. Moreover, the final key rate over transmission distance is simulated. For the low dark count of the HSPS and the utilization of the two-photon pulses, our protocol has a higher key rate and a longer transmission distance than any other decoy state protocol.