We observed an unconventional parity-violating vortex in single domain Sr2RuO4 single crystals using a transport measurement. The current-voltage characteristics of submicron Sr2RuO4 shows that the induced voltage has anomalous components which are even function of the bias current. The results may suggest that the vortex itself has a helical internal structure characterized by a Hopf invariant (a topological invariant). We also discuss that the hydrodynamics of such a helical vortex causes the parity violation to retain the topological invariant.