Precise identification and in-depth understanding of defects in nanomaterials can aid in rationally modulating defect-induced functionalities. However, few studies have explored vacancy defects in ligand-stabilized metal nanoclusters with well-defined structures, owing to the substantial challenge of synthesizing and isolating such defective metal nanoclusters. Herein, a novel defective copper hydride nanocluster, [Cu36H10(PET)24(PPh3)6Cl2] (Cu36; PET: phenylethanethiolate; PPh3: triphenylphosphine), is successfully synthesized at the gram scale via a simple one-pot reduction method. Structural analysis reveals that Cu36 is a distorted half cubic nanocluster, evolved from the perfect Nichol's half cube. The two surface copper vacancies in Cu36 are found to be the principal imperfections, which result in some structural adjustments, including copper atom reconstruction near the vacancies as well as ligand modifications (e.g., substitution, migration, and exfoliation). Density functional theory calculations imply that the above-mentioned defects have a considerable influence on the electronic structure and properties. The modeling suggests that the formation of defective Cu36 rather than the perfect half cube is driven by the enlargement of the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital of the nanocluster. The structural evolution induced by the surface copper atom vacancies provides atomically precise insights into the defect-induced readjustment of the local structure and introduces new avenues for understanding the chemistry of defects in nanomaterials.