Protein-aptamer interactions have been used in a wide range of fields, including medical diagnosis and protein delivery. Herein, we report a method for thrombin delivery with thrombin-binding aptamer (TBA), which is one of the well-known aptamers for thrombin, by generating giant thrombin nanoparticles (GTNPs). GTNPs can be synthesized by crosslinking thrombin with DNA nanostructures that possess several TBA molecules. To generate GTNPs, two different DNA nanostructures were used. Y-shaped DNA with TBA and X-shaped DNA with TBA were used for 250 and 650 nm GTNPs, respectively. Controlled release of thrombin from GTNPs was performed by adding complementary DNA (cDNA) to TBA. To investigate thrombin release from GTNPs, the sizes of the GTNPs were measured using dynamic light scattering, atomic force microscopy (AFM), and scanning electron microscopy (SEM). We confirmed a decrease in the size of GTNPs with various concentrations of cDNA, suggesting the release of thrombin. Based on these results, we expect that our method can be used to control the amount of thrombin released effectively. Our method is also widely applicable for effective protein delivery.