Our mind is organized hierarchically, it is the result of the try and error process of evolution.  We don't know how is Nature, we can only make best possible predictions for our survival.

The brain's neurological structure is hierarchically structured and interconnected.

All biological organisms have hierarchical structure: atoms, molecules, cells, organelles, organs, body.

Nature is also fundamentally hierarchical: subatomic particles, atoms, macroscopic systems, stars and stellar systems, galaxies, galactic groups/clusters/superclusters. We observe this scientifically, taking into account the limits of our observational capabilities.

I am not sure that anyone has ever really explained this self-evident hierarchical organization. Mostly we seem to ignore the issue because of our reductionist assumptions and our proclivity to focus on limited parts of nature, rather than trying to understand all of nature's scales/systems in one unified model.

My tentative approach to explaining the hierarchies we observe in many natural systems is that nature's geometry is often conformal geometry that does not involve absolute lengths, but preserves angles. This geometry lends itself to self-similar hierarchies, i.e., fractal phenomena that are ubiquitous in nature.

Compositeness is not hierarchy, a galaxy is a set of elementary particles in interaction, like every physical system.  Hierarchy is for instance thermodynamics, that describes a system regardless of the details.

On the other hand, the goal of the human intelligence is not to extract truth about the working of Nature, it is to extract information from the environment that is necessary for survival.  Then, the perceptions aren't analytical, but are built for recognizing objects, forms, sounds, materials etc.  That is, the information that is useful for survival is hierarchical.  A thermodynamical variable has no more reality that the one that we give to it.  For example temperature is the variable that avoid to be burned, while physically it is but the agitation of the constituent particles.