The Beal′s eyed turtle (Sacalia bealei) is critically endangered in China. We conducted a study on their population distribution and habitat selection at Huboliao National Nature Reserve in Fujian Province (24°30′05″N﹣24°56′20″N, 117°12′42″E﹣117°22′45″E) from August 2014 to October 2015 by cage trapping method based on the knowledge we got from the local people. The relative population density of Beal′s eyed turtle was 0.003/cage day. Five turtles were captured from the stream primary tributary and no any individuals were captured in the main stream and secondary tributary. We set 30 plots with 10 ×10 m2 each to collect the habitat characteristics in the the main stream, primary and second tributary to compare the variation of 21 ecological factors between them. The ecological factors such as number of woody plant species, thickness of deciduous leaves, percentage of exposed stones, slope and water depth were analyzed by One-way ANOVA, vegetation type, soil type, substrate type and obscured object type were analyzed by Chi-square test, while woody plant density, crown density, number of benthos species, number of benthos density, distance to human disturbance, elevation, number of stone caves, flow water speed, stream width, fruiter abundance, number of herbage species and herbage density were analyzed by Kruskal-Wallis Test with the paired-comparisons. A significant difference was detected for 13 factors between the primary tributary and main stream, and for 16 factors between the primary and secondary tributary (Table 1). These result indicated that the Beal′s eyed turtle prefer the habitat of primary tributary due to it providing a larger shelters, more plentiful fruiter, more ovipositing sites and far from human disturbance. The habitat of the primary tributary had following characteristics: longer distance to human disturbance (250.17 ± 27.03 m), medium elevation (276﹣389 m), mild slope (18.50° ± 2.21°), medium water depth (3.86 ± 0.17 m), larger canopy density (50.10% ± 3.56%), higher fruiter abundance (1.40 ± 0.20 ind/m2), deeper deciduous leaves (4.97 ± 0.16 cm), more stony substrate, more stone caves (0.26 ± 0.02 /m2) ,more percentage of exposed stones (47.10% ± 2.27%), higher density (5.03 ± 0.35 ind/m2) and species richness of benthos (3.97 ± 0.26 /m2). In order to assure the sustainable survival of Beal′s eyed turtle, we provided conservation suggestions, such as forest conservation and anti-poaching would be conducted immediately.