This subspecies is notable for its red phase coloration, although slate-grey and dull-lavender specimens are not uncommon. It prefers upland habitats such as sand hills and longleaf pine savannas, and may occasionally be found in the foothills of South Carolina and Georgia, with rare populations moving through the mountains of Georgia into Alabama. However, recent reports have concluded that S. m. miliarius makes use of lowland environments such as hardwood bottomlands and Carolina bays.

Like other subspecies of pygmy rattlesnake, the Carolina pygmy is a primarily crepuscular species, active around dawn and dusk; and targets a wide variety of prey including small reptiles, amphibians, centipedes and small snakes. Their young also have yellow-tipped tails to lure prey.

In North Carolina, they are considered threatened due to habitat loss and illegal collection resulting from their striking coloration. A lack of disturbance events (i.e. fire suppression), resulting in soil changes and reduced hibernacula, also likely poses a threat for this species.