Nanoparticles are used extensively to detect nucleic acid biomarkers due to their analytical applicability and sensitivity. Systems employing the surface plasmon resonance of gold nanomaterials are overwhelmingly considered to be candidates. The aggregation of gold nanomaterials mediated by the hybridization of target DNA at the interface causes a change in the surface plasmon resonance inherent in gold nanomaterials. Such changes can be measured by spectroscopy or even visualized by the naked eye, enabling effective and positive detection. The optical properties of gold nanoparticles are affected by their shape. The geometric appearance of the nanoparticles also affects their colloidal stability and aggregation behavior. In this study, we examined the effect of the geometric appearance of gold nanomaterials on DNA-mediated aggregation behavior through comparative experiments. Experimental and theoretical methods were used concurrently to derive accurate results and to support the hypotheses. Coarse-grained molecular dynamics simulations were performed with a large-scale atomic/molecular massively parallel simulator to understand the aggregation of nanoparticles with the same surface area and various aspect ratios. As a result, we confirmed that the aggregation sensitivity of nanoparticles was affected by the shape of the contact point with the gold nanomaterials. This study demonstrates that the design of a detection system should be accompanied by an in-depth review of the morphology of the nanoparticle.