Abstract The study aimed to analyze the Chinese muntjac’s population resources, and to establish reasonable measures for population protection and management. We investigated the Chinese muntjac population by using traditional belt transect method and Capture-Mark-Recapture method, in Gutianshan Nature Reserve To estimate population density. In addition, the sex ratio was assessed by using genetic markers from fecal samples, which were collected during four field surveys in April 2014, July 2014, October 2014 and January 2015. The results from the belt transect method showed that the density in the whole reserve area was about （5.8±0.4）/km2 and the total population number was about 473.5±29.2. In the core area, the density was the highest（7.5±0.7）/km2, and the total number of Chinese muntjac was about 160.8±14.0. The density in the buffer area was about （5.7±0.6）/km2 and the total population was about 98.2±10.4. In the experimental area, the density of the Chinese muntjac was the lowest（3.3±0.5）/km2, and the total population was about 140.5±20.7. With the data from fecal DNA analysis, the density was estimated (4.9±0.3) /km2 across the entire reserve and the total population was 397±26. The transect sampling survey showed that, among the different functional areas, the population density varied with the change of seasons. The core area, the buffer area and experimental area had the highest population densities in spring. In the Nature Reserve Area, Chinese muntjac lived primarily at an altitude between 400 to 800 meters. In the summer, they migrated to the higher elevations, and to lower elevations in the winter. The average sex ratio of the Chinese muntjac in Gutianshan population was about 1.17:1 in different seasons, and the annual sex ratio was about 1.11:1（93♀and 84♂）（x=0.458, P=0.499）. Any advantage of more female individuals was not obvious and the protection strategy should be strengthened as much as possible in order to increase the population size.