We studied habitat selection of red deer (Cervus elaphus alxaicus) during winter 2007-08 and spring 2008 in the Helan Mountains on the border between Ningxia and Inner Mongolia Autonomous Regions. We documented deer habitat through direct observation and examination of fresh sites used by red deer located on 21 transects distributed throughout the study area. Eighteen ecological factors from 131 winter sites and 181 spring sites were measured in 15 drainages in the study area. Winter and spring habitat selection by red deer differed in most ecological factors, i.e., vegetation type, dominant tree, shrub height, distance to nearest shrubs, slope, aspect, altitude, distance to bare rock, and hiding cover. Compared with winter habitat, red deer selected spring habitats with montane conifer forest dominated by Pinus tabulaeformis and Picea crassifolia, slightly higher shrub density, shrub height, and closer proximity to shrubs and slopes, gently higher altitude at half sunny and shady side, closer to bare bock, and higher hiding cover. Canonical scores indicated that winter and spring habitats selected by red deer overlapped to some extent. However, scores for spring habitat locations were distributed widely. The Wilk′s lambda exhibited a highly significant difference in winter and spring habitat selection of red deer (Wilk’s λ = 0.683, χ2 = 116.995, df = 13, P ＜ 0.001). Discriminating variables that improved a stepwise discriminant model included (in order of importance) tree density, distance to the nearest shrubs, slope degree, altitude, distance to water resource, distance to bare rock, and hiding cover. Predicted accuracy of the model in classifying red deer habitats was 79.9%. Misclassification of spring habitats and winter habitats by red deer were 22.1% and 20.6% respectively.