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We investigate the effect of three-dimensionality on the synchronisation characteristics of the wake behind an oscillating circular cylinder at$${\textit {Re}} = 300$$. Cylinder oscillations in rotation, transverse translation and streamwise translation are considered. We utilise phase-reduction analysis, which quantifies the phase-sensitivity function of periodic flows, to examine the synchronisation properties. Here, we present an ensemble-based framework for phase-reduction analysis to handle three-dimensional wakes that are not perfectly time-periodic. Based on the phase-sensitivity functions, synchronisability to three types of cylinder oscillations is evaluated. In spite of similar trends, we find that phase-sensitivity functions involving three-dimensional wakes are lower in magnitude compared with those of two-dimensional wakes, which leads to narrower conditions for synchronisation to weak cylinder oscillations. We unveil that the difference between the phase-sensitivity functions of two- and three-dimensional flows is strongly correlated to the amplitude variation of the three-dimensional flow by the cylinder motions. This finding reveals that the cylinder motion modifies the three-dimensionality of the wake as well as the phase of vortex shedding, which leads to reduced phase modulation. The synchronisation conditions of three-dimensional wakes, predicted by phase-reduction analysis, agree with the identification by parametric studies using direct numerical simulations for forced oscillations with small amplitudes. This study presents the potential capability of phase-reduction to study synchronisation characteristics of complex flows.