Low-dimensional magnetism has long been the central issue in condensed matter physics, and van der Waals materials provide an ideal platform for exploring magnetism at the two-dimensional limit. The magnetic order in two-dimensional model materials is suppressed, and arguments based upon topology are useful for describing phases of matter. An example is the Berezinskii-Kosterlitz-Thouless transition where spin correlations over long distances eventually give rise to magnetic order; thus has never been realised experimentally in magnetic materials. A similar topological transition with vortices by chirality, handedness of the electronic spin arrangements, is possible without inducing any order; however, evidence for this higher-order vortex dissociation transition remains elusive. Here, we combine polarised neutron scattering and theoretical simulations to show that the transition occurs in a van der Waals magnet. We experimentally observe in-plane and out-of-plane spin moments, and their ratio, the spin-state anisotropy, shows a tendency for reversal across an anomalous temperature. Our simulations confirm the experimental findings; the tendency cannot be reproduced when removing the chiral vortices. The chirality-driven topological transition is general but has been challenging to be detected. Our results set a new paradigm for revealing topological characteristics with a higher-order degree of freedom.