Dual three-phase permanent magnet (DTPPM) machines are suitable for applications with high power density and high reliability requirements. However, uneven demagnetization fault (UDF) can occur due to harsh working conditions. This article proposes a non-invasive, online detection method of UDF in DTPPM machines based on the electrical signal difference between two sets of three-phase windings, which can be more conducive to UDF diagnosis with higher sensitivity. Firstly, the influence of dual three-phase winding arrangements on phase permanent magnet (PM) flux linkage is investigated in DTPPM machines under UDF. It shows that the fault characteristic harmonics appear in fractional-slot DTPPM machines and integral-slot DTPPM machines where a single set of three-phase windings is rotationally asymmetric. Further, according to the three-phase relationship of harmonic vectors, it is analyzed whether the fault characteristic harmonics are reflected in stator currents or zero-sequence voltage components (ZSVCs). Notably, taking advantage of the structural feature in DTPPM machines, the proposed method obtains higher sensitivity of UDF detection, as the amplitudes of fault characteristic harmonics in electrical signal difference are larger than that in stator current or ZSVC in a single set of three-phase windings. Finally, experiments are conducted to validate the effectiveness of the proposed method.