An interesting 48-metal Zn(II)-Yb(III) nanocluster (1) with a size of about 1.3 × 2.8 × 3.1 nm was constructed by carbonate templates from a Schiff base ligand. It exhibits ligand-centered emission and near-infrared (NIR) luminescence of Yb(III), which are used in the dual-emissive detection of rutin (Rut) with high sensitivity even in the presence of other interferences. The response behavior can be expressed by the second-order equation I980 nm/I510 nm = A*[Rut]2 + B*[Rut] + C, and the limits of detection to Rut for the emissions of 1 are 2.23 μM and 0.20 nM.