We study the chiral effective theory in the presence of QCD vortices. Gauge invariance requires novel terms from vortex singularities in the gauged Wess-Zumino-Witten action, which incorporate anomaly induced currents along the vortices. We examine these terms for systems with QCD axial domain-walls bounded by vortices (vortons) under magnetic fields. We discuss how the baryon and the electric charge conservations are satisfied in these systems through interplay between domain-walls and vortices, which manifests Callan-Harveys mechanism of the anomaly inflow.