DNA tetrahedron nanostructure (DTN) is one of the simplest DNA nanostructures and has been successfully applied for biosensing, imaging, and treatment of cancer. To facilitate its biomedical applications and potential clinical translation, fundamental understanding of DTN's transportation among major organs in living organisms becomes increasingly important. Here, we describe the efficient renal clearance of DTN in healthy mice by using positron emission tomography (PET) imaging. The kidney elimination of DTN was later applied for renal function evaluation in murine models of unilateral ureteral obstruction (UUO). We further established a mathematical program of DTN to validate its changes of transportation pattern in healthy and UUO mice. We believe the establishment of pharmacokinetic profiles and mathematical model of DTN may provide insight for future optimization of DNA nanostructures for biomedical applications.