The directed self-assembly strategy endows the ultrasmall metal nanocluster (MNC, <3 nm) superstructure assemblies with enhancement of inherent characteristics or generation of novel properties, which has aroused great interests in multidisciplinary applications, including catalysis, bioimaging, and optics. However, the precise synthesis of ultrastable hydrophilic MNC assemblies remains a challenge. Herein, rationally designed star-like polymer unimolecular micelles were used as scaffold nanoreactors for the precise in situ confined synthesis of hydrophilic spherical MNC superstructure assemblies (Au, Ag, Cu, Pt, and AuAg alloy) in aqueous solution. By effectively proceeding with photoinduced atom transfer radical polymerization (photoATRP), the size of the MNC assembly could be precisely customized. The thiolate ligands were utilized to control the ultrasmall size of single MNCs and greatly improve the catalytic stability via the bridging interaction with the polymer template. Moreover, deep red to NIR emitting photoluminescent MNC assemblies could be realized via adjusting the aggregation-induced emission properties of the Au(I)-SR complex motif and the molecular weight of the polymer template. Thus, we anticipate that this strategy may contribute a practical solution to broadly create hydrophilic ultrastable well-defined MNC assemblies with many unforeseen properties in a precise way for applications in catalysis, optics, and biology fields.