Controlled spatial arrangements of superparamagnetic iron oxide nanoparticles (SPIONs) in complex nanostructures determine fine tuning of physico-chemical properties which, in turn, may lead to new practical applications. We report here on newly observed properties of hierarchical SPIONs nanostructure with bundle-like morphology, also known as nanobundles. Colloidal chemical processes and sol-gel synthesis were used for the synthesis of nanobundles, i.e. i) self-assembly of SPIONs into magnetic nanoparticle clusters, ii) their magnetic assembly to the nanochains, and finally iii) formation of bundle-like hierarchical nanostructure. An XRPD measurements show spinel crystal structure of maghemite/magnetite nanoparticles, EDS analysis reveals Fe, Si and O as main elements whereas SEM/TEM analysis show silica-coated magnetic nanoclusters (∼100 nm) and their hierarchical assemblies with bundle-like morphology of ∼8 μm length and ∼1 μm width. TEM analysis revealed core-shell nature of iron oxide nanoparticle clusters with their size of around 80 nm that were coated by an amorphous silica shell with thickness of ∼15 nm. The nanoclusters in the core are constructed of maghemite/magnetite nanoparticle assembly with primary iron oxide nanoparticle size about 10 nm. The magnetization M data as a function of an applied external magnetic field H were successfully fitted by the Langevin function, whence the magnetic moment μp = 19256 μB, and the diameter d = 9.6 nm of nanoparticles were determined. Microsized bundle-like particles are superparamagnetic, magnetically guidable and possess high transverse relaxivity of r2 = 397.8 mM−1s−1. Magnetic properties and such high value of transverse relaxivity holds promise for nanobundles application in MRI imaging (MRI contrast agent), as nanobundles may enhance the magnetic field in their surroundings and enhance proton relaxation processes. Our nanobundles can open new opportunities in the biomedical applications, magnetic separation, photonic crystals and magnetic liquid manipulation and can be inspiration for synthesizing novel self-assembled nanoparticle structures.