The inertia identification accuracy of the conventional orthogonal principle-based (OP-based) method is degraded due to the speed harmonic. The error analysis shows that it resulted from the harmonics of the estimated angular acceleration and disturbance torque in the embedded disturbance observer. To solve this issue, this paper proposes a robust inertia identification method designed with a dedicated disturbance observer accounting for speed harmonic, which is essentially designing the transfer functions of the estimated angular acceleration and disturbed torque in such a way that their harmonics are reduced effectively, therefore, the inertia identification error can be significantly reduced. Furthermore, the influence on the inertia identification from the coefficients of the disturbance observer is analyzed and the inertia identification block diagram of the dual three-phase permanent magnet synchronous machine (DTP-PMSM) drive system is presented. The feasibility and effectiveness of the proposed approach are verified by experiments. For the prototype DTP-PMSM, the inertia identification error decreases from 43.9% to 2.7% at half-rated load and 60 rpm, from 49.6% to 7.5% at rated load and 60 rpm, from 33.4% to 1.7% at half-rated load and 120 rpm, and from 40.9% to 6.6% at rated load and 120 rpm.