With the promotion of high voltage direct current (HVDC) system construction around the world, the series-connected multi-pulse rectifiers (SCMPRs) have been widely used in high-power rectifying occasions in the power system. Since the certain order of harmonics cannot be effectively eliminated under the non-ideal conditions, many different phenomena, such as the unbalance of supply voltage and line/transformer parameters, the influence of background harmonics, and the non-equidistance of thyristor triggering pulses, may cause the non-characteristic harmonics (NCHs) of SCMPR. However, the existing frequency-domain harmonic model cannot be used to analyze the harmonic characteristics of the SCMPRs under non-ideal conditions. In this paper, a general frequency-domain harmonic coupling matrix model (HCMM) is proposed. The proposed HCMM can consider most of the above imbalance factors and the model can explicitly illustrate the harmonic coupling relationship between the SCMPRs supplied voltage and the generated harmonic currents. The generality of the SCMPR model under non-ideal conditions is improved accordingly. The HCMM is simplified by comparing and analyzing the effects of the transformer structure and parameters. Moreover, by analyzing the harmonic generation characteristic of the negative-sequence component, the HCMM can be further simplified. Finally, time-domain simulation and lab experimentation are performed to verify the accuracy and efficiency of the frequency-domain HCMM of SCMPRs. The results prove the generality of the proposed model and also illustrate the harmonic generating influence of unbalanced parameters from the transformer and supply voltage.