Metal nanoclusters (NCs) possess unique optical properties, and exhibit a wide variety of potential applications. DNA with robust molecular programmability is demonstrated as an ideal scaffold to regulate the formation of NCs, offering a rational approach to precisely tune the spatial structures of NCs. Herein, the first use of branched DNA as scaffold to regulate the formation of silver nanoclusters (super-AgNC) is reported, in which the spatial structures are precisely designed and constructed. Super-AgNC with tunable shapes and arm-lengths including Y-, X-, and (Y-X)- shaped super-AgNC is achieved. The molecular structures and optical properties of super-AgNCs are systemically studied. As a proof of application, remarkably, super-AgNCs exhibit superior antibacterial performance. In addition, super-AgNCs show excellent biocompatibility with three types of tissue cells including 293T (human embryonic kidney cells), SMCs (vascular smooth muscle cells), and GLC-82 (lung adenocarcinoma cells). These performances enable the super-AgNCs adaptable in a variety of applications such as biosensing, bioimaging, and antibacterial agents.