We have developed a simple and flexible chemical method to synthesize orderly metallic nanoaggregates using a designed SiO2-Au core-shell building block. The number of the building blocks in a nanoaggregate is tunable from one to three. These metal narrostructures can generate an enlarged localized electromagnetic field through surface plasmon resonance and enhance the optical signals of the photoactive molecules within this electromagnetic field. Aggregates of metallic nanoparticles provide a higher signal enhancement than well-dispersed nanoparticles combined. The level of signal enhancement is determined by the number of building blocks in a nanoaggregate. The signal enhancement of the nanoaggregates has been verified with a near-infrared (NIR) dye. In the NIR region, biological samples have low background signals and deeper penetration of radiation. The application of these NIR enhanced metal nanostructures will open a significant approach for sensitive detection of bioloaical samples.