The paper presents the numerical calculation of iron loss in a novel axial flux machine with segmented armature torus topology is researched. Firstly, the new machine concept and the iron loss model derived from Bertotti's formula are introduced, which subdivides the total iron losses into 3 components: hysteresis losses, eddy current losses and excess losses. The coefficients of the iron loss model are estimated from the measurement data of iron loss at various frequencies and different levels of magnetisation using a curve fitting method. The real waveform of flux density is far from sinusoidal, which is assumed in the Bertotti's formula. Besides, the distribution of flux density in each element is completely different. In order to solve the problems, the Fourier transformation of flux density waveform in each finite element is performed, which requires the complete waveform for a whole electrical period. The total iron loss in the motor is determined as the sum of the iron loss in each element. In order to reduce the computation time, the determination of complete flux density waveform from analysis over one-sixth electrical period is researched. Moreover, for the further reduction of the calculation time the replacing of transient analysis with stationary analysis is also investigated. Finally, the results of iron losses founded on the transient and stationary analysis are compared.