Ultrafine face‐centered cubic (fcc) ruthenium nanoclusters (NCs) are of great interest due to their super high catalytic activity. However, it is extremely difficult to prepare ≈1 nm fcc ruthenium NCs with high energy atoms due to their easy aggregation. Herein, the nucleation process of ruthenium centers by confined pyrolysis of a multivariate metal–organic framework to isolate ultrafine fcc NCs (from single atom to 1.33 nm) via in situ formed stabilizers is unveiled. Systematic investigations demonstrate that preferential nucleation of Ru single atoms to fcc clusters in the initial nucleation represents a key step and makes it possible to separate ultrafine fcc Ru NCs with in situ formed N‐doped porous carbon. A record high turnover frequency of 1300.53 min−1 for methanolysis of ammonia borane is achieved by 1.33 nm NCs. This work suggests a new strategy to prepare ultrafine metal NCs by instantly capturing structure‐specific crystal nuclei with in situ formed stabilizers. The nucleation process of Ru centers is unveiled by confined pyrolysis of a multivariate metal–organic framework. The preferential nucleation of Ru single atoms to face‐centered cubic clusters in the initial nucleation suggests a new strategy to prepare ultrafine metal nanoclusters (from single atom to 1.33 nm) by instantly capturing structure‐specific crystal nuclei with in situ formed stabilizers.