Extending of nanostructures into the third dimension has become a major research avenue in condensed-matter physics, because of geometry- and topology-induced phenomena. In this regard, superconductor 3D nanoarchitectures feature magnetic field inhomogeneity, non-trivial topology of Meissner currents and complex dynamics of topological defects. Here, we investigate theoretically topological transitions in the dynamics of vortices and slips of the phase of the order parameter in open superconductor nanotubes under a modulated transport current. Relying upon the time-dependent Ginzburg–Landau equation, we reveal two distinct voltage regimes when (i) a dominant part of the tube is in either the normal or superconducting state and (ii) a complex interplay between vortices, phase-slip regions and screening currents determines a rich FFT voltage spectrum. Our findings unveil novel dynamical states in superconductor open nanotubes, such as paraxial and azimuthal phase-slip regions, their branching and coexistence with vortices, and allow for control of these states by superimposed dc and ac current stimuli.