The lined pocket mouse is smaller than most pocket mice in the genus Chaetodipus, averaging in total length including a tail of. It resembles Nelson's pocket mouse in size and general appearance but lacks the stiff spines that that species has among the hairs on its rump. Its coloring is also distinctive; the dorsal surface is gray faintly lined with buff giving a drab appearance, the sides are gray and the underparts are white, with a fine buff line delineating the margin between sides and belly.
The lined pocket mouse lives in a burrow and is nocturnal. The entrance of the burrow is usually at the base of a plant, in a crevice or in some other concealed location. When it emerges after dark, the pocket mouse moves slowly around staying under cover as much as possible. If it needs to cross an open space it moves much more rapidly. It feeds on seeds such as those of the prickly pear which fall to the ground, but it does not eat the pulp of the cactus fruit.