Ganjiang River originates from the western foot on the southern range of the Wuyi Mountains in China. The unique geographical environment and climatic characteristics formed a rich diversity of amphibian species for Ganjiangyuan area of Jiangxi Province in China. However, the investigations on the composition and species diversity of amphibian community in this area are very scarce at present. This is not conducive for the conservation of amphibian species diversity in the source area of Ganjiang River. In this study, we investigated the resource status of amphibian and its characteristics of community composition and species diversity using the line transect method in the Ganjiangyuan area of Jiangxi Province from April to September 2016. Subsequently, we compared their differences among three habitats of mountain forest area, hilly forest and farmland area, and basin farmland area. The three habitats were 8-30 km apart from each other, and 10 sample lines with a length of 200-300 m and a spacing distance of more than 500 m were respectively arranged on each habitat. The results of our investigations showed that the Ganjiangyuan area had 23 amphibian species belonging to 8 families with Fejervarya multistriata and Microhyla fissipes as the dominant species. Meanwhile, we added 3 new amphibian species recorded in the Ganjiangyuan area, including Occidozyga lima, Rana hanluica and Quasipaa jiulongensis. There were significant seasonal and habitat differences in the composition and species diversity of the amphibian community in the Ganjiangyuan area. Seasonal reproduction of amphibian was the major factor causing the seasonal difference, while factors such as land use types, habitat features, spatial distance, and species habits led to the habitat difference. Therefore, the species richness and diversity index in spring and summer were higher than those of autumn; the amphibian species richness and diversity index were the highest in the mountain forest area, followed by the basin farmland area, and the lowest in the hilly forest and farmland area. The mountain forest area should be the priority area for the conservation of amphibian diversity in the Ganjiangyuan area. Hoplobatrachus chinensis, a national second-class protected animal species of China, was distributed in all of the three habitats, with more individuals in the basin farmland area and the mountain forest area, but the endangered species was exposed to a bigger threat in the basin farmland area. Therefore, it was suggested to strengthen the conservation of H. chinensis and its habitat in the basin farmland area.