Abstract In the known field of topological photonics, what remains less so is the breakdown effect of topological phases deteriorated by perturbation. In this study, the authors investigate the variance on topological invariants for a periodic Kekulé medium perturbed in unit cells, which was a gyromagnetic photonic crystal holding topological phases induced by synchronised rotation of unit cells. Two parameters for geometric and material perturbation are respectively benchmarked to characterise the topological degradation. Our calculation demonstrates that such a periodic perturbation easily destructs the topological phase and thus calls for further checkups on robustness under such unit‐cell‐perturbation in realisation.