This article proposes an improved digital discrete-time current control scheme for a dual three-phase flux-switching permanent-magnet (FSPM) machine with significant asymmetry between two sets of armature windings. Resonant controllers have been widely used to eliminate current harmonics and unbalance for multiphase machine. However, when the harmonic frequency is relatively high with respect to the sample frequency, the discretization of resonant controller needs additional pole correction and delay compensation, making the design more complicated and performance degraded. In this article, based on the discrete-time domain machine model, the resonant controllers directly designed in z domain using pole-zero cancelation method are developed and optimized for the practical implementation. These resonant controllers can be applied in either stationary frame or rotational frame and the stability is permitted in a wide frequency range. Experimental results on a prototype dual three-phase FSPM machine validate the effectiveness of the proposed scheme.