A versatile DNA bipyramid nanostructure is assembled as a tumor-targeted, dual-modal nanoprobe for in vivo imaging. Magnetic resonance contrast agents (Gd-DOTA), fluorescence imaging molecules (Dylight800), and tumor-targeting moieties (anti-EGFR aptamers) were precisely organized on the DNA bipyramid platform. DNA bipyramids coated by polyethylene glycol-polylysine copolymer showed enhanced resistance against digestion in serum and prolonged circulation time in vivo. The multifunctional DNA bipyramid improved codelivery of magnetic resonance/fluorescence imaging (MR/FI) contrast agents to triple-negative breast tumors, realizing noninvasive tumor imaging without observable systemic toxicity. Our rationally designed DNA-based platform will prove powerful to develop customized molecular probes for cancer diagnosis.