We studied the seasonal habitat selection of the red deer, Cervus elaphus alxaicus Bobrinskii & Flerov, 1935, in the Helan Mountains, China, from December 2007 to December 2008. Habitat selection varied widely by season. Seasonal movements between high and low elevations were attributed to changes in forage availability, alpine topography, the arid climate of the Helan Mountains, and potential competition with blue sheep, Pseudois nayaur (Hodgson, 1833). The use of vegetation types varied seasonally according to food availability and ambient temperature. Red deer used montane coniferous forest and alpine shrub and meadow zones distributed above 2,000 m and 3,000 m in summer, alpine shrub and meadows above 3,000 m in autumn, being restricted to lower elevation habitats in spring and winter. The winter habitat of C. elaphus alxaicus was dominated by Ulmus glaucescens Franch. and Juglans regia Linnaeus, deciduous trees, and differed from the habitats selected by other subspecies of red deer. Cervus elaphus alxaicus preferred habitats with abundant vegetation coverage to open habitats in winter, but the reverse pattern was observed in summer and autumn. Red deer preferred gentle slopes (<10°) but the use of slope gradient categories varied seasonally. Red deer avoidance of human disturbance in the Helan Mountains varied significantly by season. Information on red deer habitat selection can help understand the factors affecting seasonal movements and also support decision making in the management and conservation of red deer and their habitats.