This study proposes a generic mathematical modelling and decoupling fault-tolerant vector control for dual three-phase permanent magnet synchronous machine (PMSM) with one phase open based on the conventional dual three-phase voltage source inverters, accounting for the mutual coupling between two sets of three-phase windings and the second harmonic inductance. When the dual three-phase PMSM has one phase open, the permanent flux-linkages are asymmetric and there are second harmonic components in the conventional synchronous reference frame (dq-frame). Based on the proposed mathematical modelling, both permanent magnet flux-linkages and currents become DC values in the dq-frame, and therefore, the conventional proportional integral (PI) controller can be used to regulate the dq-axis currents. Then, a decoupling fault-tolerant vector control with/without a dedicated feed-forward compensation is proposed to validate the correctness of the proposed mathematical modelling. Experimental results on a prototype dual three-phase PMSM with one phase open show that the second harmonic dq-axis currents can be well suppressed simply by the conventional PI controller and dedicated feed-forward compensation. It also shows that the decoupling fault-tolerant control based on the proposed modelling and control method has excellent dynamic performance, which is equivalent to the vector space decomposition control for the healthy machine.