It was formerly considered a subspecies of the desert pocket mouse (C. pencillatus), but was determined to be a distinct species in 1996, following analysis of its mitochondrial DNA.

[3] Chihuahuan pocket mice are moderately sized rodents, with a total adult length of 16 to 18 centimetres (6.3 to 7.1 in), including the tail, and weighing 15 to 23 grams (0.5 to 0.8 oz).

The hairs on the rump are long and slender, but there are no spines, such as are present on the otherwise very similar rock pocket mouse.

They are nocturnal, spending the day in burrows comprising a central chamber from which numerous tunnels fan out to separate openings on the surface.

It inhabits desert scrubland, preferring areas with soft or sandy soil, although it may occasionally be found in grassland or by river banks.