The aim of this paper is to describe the development and application of a multi-frequency harmonic balance solver for GPUs, particularly suitable for the simulation of periodic unsteadiness in nonlinear turbomachinery flows comprised of a few dominant frequencies, with an unsteady multistage coupling that bolsters the flow continuity across the rotor/stator interface. The formulation is addressed with the time-domain reinterpretation, where several non-equidistant time instants conveniently selected are solved simultaneously. The set of required frequencies in each row is driven into the governing equations with the help of almost-periodic Fourier transforms for time derivatives and time shifted boundary conditions. The spatial repetitiveness inside each row can be exploited to perform single-passage simulations and the relative circumferential positioning of the rotors or stators and the different blade or vane counts is tackled by means of adding fictitious frequencies referring to non-adjacent rows therefore taking into account clocking and indexing effects. Existing multistage row coupling techniques of harmonic methods rely on the use of non-reflecting boundary conditions, based on linearizations, or time interpolation, which may lead to Runge phenomenon with the resulting numerical instabilities and non-preserving flux exchange. Different sets of time instants might be selected in each row but the interpolation in space and time across their interfaces gives rise to robustness issues due to this phenomenon. The so-called synchronized approach, developed in this work, consist of having the same time instances among the whole ensemble of rows, ensuring that flux transfer at sliding planes is applied more robustly. The combination of a set of shared non-equidistant time instances plus the use of unequal frequencies (real and fictitious) may spoil the Fourier transforms conditioning but this can be dramatically improved with the help of oversampling and instants selection optimization. The resulting multistage coupling naturally addresses typical numerical issues such as flow that might reverse locally across the row interfaces by means of not using boundary conditions but a local flux conservation scheme in the sliding planes. Some examples will be given to illustrate the ability of this new approach to preserve accuracy and robustness while resolving them. A brief analysis of results for a fan stage and a LPT multi-row case is presented to demonstrate the correctness of the method, assessing the impact in the modeling accuracy of the present approach compared with a time-domain conventional analysis. Regarding the computational performance, the speedup compared to a full annulus time-domain unsteady simulation is a factor of order 30 combining the use of single-passage rows and time spectral accuracy. © 2020 ASME.