Bed-site selection is the behavioral adaptation of wild animals to their ecological environment. In this study, we explored the seasonal variation of nocturnal bed-site characteristics by Milu (Elaphurus davidianus, Père David’s deer). We used direct and track observation methods to assess nocturnal bed-site selection over different seasons (November 2013 to December 2014) by Milu in Hubei Shishou Milu National Nature Reserve, China. We recorded the ecological characteristics of 184 nocturnal bed-site plots and 184 control plots. Results showed that Milu preferred bed-sites with greater woodland cover, a greater proportion of vegetation, abundant food resources, and proximity to shelter (reeds or woods) during spring, autumn and winter (P < 0.05). Moreover, differences in distance to roads and to human settlements in bed-sites selection were not significantly different (P > 0.05) during spring and autumn. In summer, the Milu population preferred bedding on bare ground characterized by a low hiding cover, higher herbage coverage, lower food abundance, close proximity to hide and water, and an increased distance to road and human settlement (P < 0.05). This is in contrast to winter, as the Milu population preferred bed-sites with lower wind speeds that were closer to roads and human settlements (P < 0.05). Stepwise discriminant analysis indicated that seasonal nocturnal bed-site selection by the Milu population could be discriminated with three canonical discriminant functions. A Fisher discriminant function composed of herbage coverage, food abundance, hiding cover, wind speed, and distance to hide and water could discriminate the seasonal nocturnal bed-site of the Milu population. The characteristics of bed-sites selected by Milu in different seasons had some similarities and differences, most likely as a result of food, water, temperature, and anthropogenic interference. On the basis of our findings, we suggest to expand supplementary feed base, to retain vegetation that provide adequate cover for Milu, to reduce anthropogenic interference and to regulate water levels in the oxbow around the nature reserve for the conservation of Milu in this area.