Topological vortices with swirling ferroelectric, magnetic and structural anti-phase relationship in hexagonal RMnO3 (R = Ho to Lu, Y, and Sc) have attracted much attention because of their intriguing behaviors. Herein, we report the structure of multiferroic vortex domains in YMnO3 at atomic scale using state-of-the-art aberration-corrected scanning transmission electron microscopy (STEM). Two types of displacements were identified among six domain walls (DWs); six translation-ferroelectric domains denoted by α+, γ-, β+, α-, γ+ and β-, respectively, were recognized, demonstrating the interlocking nature of the anti-vortex domain. We found that the anti-vortex core is about four unit cells wide. In addition, we reconstructed the vortex model with three swirling pairs of DWs along the [001] direction. These results are very critical for the understanding of topological behaviors and unusual properties of the multiferroic vortex.