This paper studies on the permanent magnets configuration on the transmission torque of the multi-pole bilayer magnetorheological (MR) coupling. Based on the electromagnetic field theory, the magnetic circuit models of traditional permanent magnet array (TPMA) and Halbach permanent magnet array (HPMA) are established, and the magnetic flux density within the MR fluid working gaps has been derived in order to evaluate the merits of the designed MR coupling. A 3D FE magnetic-fluid analysis has been necessary following the initial conceptual analysis, in order to study the influence of key parameters on the transmission torque. The results show that the transmission torque of the MR coupling with Halbach permanent magnet array is 33.45% higher than that of the ordinary permanent magnet array, with a same structure size. For the MR coupling with Halbach permanent magnet array, the unilateral magnetic focusing effect is better with the increase of the residual flux density of the secondary magnetic pole as well as the radial length of magnetic pole. And the single side magnetic focusing effect is the best when the main magnetic pole is 15°. The influence of the magnetic pole angle on the transmission torque has been further studied.