Herein, a remarkable achievement in the synthesis and characterization of an atomically precise copper‐hydride nanocluster, [Cu41(SC6H3F2)15Cl3(P(PhF)3)6(H)25]2− via a mild one‐pot reaction is presented. Through X‐ray crystallography analysis, it is revealed that [Cu41(SC6H3F2)15Cl3(P(PhF)3)6(H)25]2− exhibits a unique shell–core–shell structure. The inner Cu29 kernel is composed of three twisted Cu13 units, connected through Cu4 face sharing. Surrounding the metal core, two Cu6 metal shells, resembling a protective sandwich structure are observed. This arrangement, along with intracluster π···π interactions and intercluster C─H···F─C interactions, contributes to the enhanced stability of [Cu41(SC6H3F2)15Cl3(P(PhF)3)6(H)25]2−. The presence, number, and location of hydrides within the nanocluster are established through a combination of experimental and density functional theory investigations. Notably, the addition of a phosphine ligand triggers a fascinating nanocluster‐to‐nanocluster transformation in [Cu41(SC6H3F2)15Cl3(P(PhF)3)6(H)25]2−, resulting in the generation of two nanoclusters, [Cu14(SC6H3F2)3(PPh3)8H10]+ and [Cu13(SC6H3F2)3(P(PhF)3)7H10]0. Furthermore, it is demonstrated that [Cu41(SC6H3F2)15Cl3(P(PhF)3)6(H)25]2− exhibits catalytic activity in the hydrogenation of nitroarenes. This intriguing nanocluster provides a unique opportunity to explore the assembly of M13 units, similar to other coinage metal nanoclusters, and investigate the nanocluster‐to‐nanocluster transformation in phosphine and thiol ligand co‐protected copper nanoclusters.