Controlling the heterogeneous nucleation of new phases is of importance in tuning the microstructures and properties of materials. However, the role of vacancy—a popular defect in materials that is hard to be resolved under conventional electron microscopy—in the heterogeneous phase nucleation remains intriguing. Here, this work captures direct in situ experimental evidences that vacancy clusters promote the heterogeneous hydride nucleation and cause the anomalous precipitation memory effect in zirconium. Both interstitial and vacancy dislocation loops form after hydride dissolution. Interestingly, hydride reprecipitation only occurs on those vacancy loop decorated sites during cooling. Atomistic simulations reveal that hydrogen atoms are preferentially segregated at individual vacancy and vacancy clusters, which assist hydride nucleation, and stimulate the unusual memory effect during hydride reprecipitation. The finding breaks the traditional view on the sequence of heterogeneous nucleation sites and sheds light on the solid phase transformation related to vacancy‐sensitive alloying elements.