The decoherence of quantum objects is a critical issue in quantum science and technology. It is generally believed that stronger noise causes faster decoherence. Strikingly, recent theoretical work suggests that under certain conditions, the opposite is true for spins in quantum baths. Here we report an experimental observation of an anomalous decoherence effect for the electron spin-1 of a nitrogen-vacancy centre in high-purity diamond at room temperature. We demonstrate that, under dynamical decoupling, the double-transition can have longer coherence time than the single-transition even though the former couples to the nuclear spin bath as twice strongly as the latter does. The excellent agreement between the experimental and theoretical results confirms the controllability of the weakly coupled nuclear spins in the bath, which is useful in quantum information processing and quantum metrology.