保护区气候温和湿润、具有典型的中亚热带湿润季风气候特点，年均降雨量1698.2—2024.4毫米。
其中，国家重点保护植物有19种，其中国家一级保护植物3种，如南方红豆杉、伯乐树、银杏等；国家二级保护植物16种，分别是苏铁、水杉、榧树、凹叶厚朴、樟树、闽楠、浙江楠、野菱、金荞麦、野大豆、花榈木、半枫荷、光叶榉、香果树、喜树、金毛狗。
据《江西赣江源国家级自然保护区综合科学考察集》所载,赣江源自然保护区内种子植物丰富，现已查明，有5个植被型组，13个植被型，87个群系，森林覆盖率94.2%，森林蓄积量748755立方米。有高等植物252科837属2582种，其中种子植物有169科686属2261种，蕨类植物35科75属216种，苔藓植物48科76属105种。
另外有被列入《中国植物红皮书》（第一批）的种类12种，被列入《濒危野生动植物国际贸易公约（CITES）附录II（2007）》的有2科29种，被列入国际自然保护同盟（IUCN，2007）《物种红色名录》的有21种，被列入《中国物种红色名录（2007）》的有52种，江西省级重点保护植物（1994年第一批，2005年第二批）的有98种。
The protected area boasts a mild and humid climate, typical of the Central Asian tropical moist monsoon climate, with an average annual rainfall ranging from 1698.2 to 2024.4 millimeters.
Among these, there are 19 species of plants under national key protection, including 3 first-class protected plants such as Southern Yew, Barley Tree, and Ginkgo biloba; and 16 second-class protected plants, which include Cycas revoluta, Metasequoia glyptostroboides, Torreya grandis, Magnolia officinalis var. biloba, Cinnamomum camphora, Phoebe chekiangensis, Phoebe bournei, Trapa natans, Fagopyrum esculentum, Glycine soja, Ormosia hosiei, Liquidambar acalycina, Zelkova serrata, Cladrastis lanceolata, Meliosma oldhamii, and Camptotheca acuminata.
According to the "Comprehensive Scientific Investigation Report on the Jiangxi Ganjiangyuan National Nature Reserve," the reserve is rich in seed plants. It has been identified that there are 5 vegetation types, 13 vegetation forms, 87 floras, a forest coverage rate of 94.2%, and a forest volume of 748,755 cubic meters. There are 252 families, 837 genera, and 2582 species of higher plants, including 169 families, 686 genera, and 2261 species of seed plants, 35 families, 75 genera, and 216 species of ferns, and 48 families, 76 genera, and 105 species of bryophytes.
Additionally, there are 12 species listed in the "Red Data Book of Chinese Plants" (First Edition), 2 families and 29 species listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Appendix II (2007), 21 species listed in the IUCN Red List of Threatened Species (2007), and 52 species listed in the "Red List of Chinese Species" (2007). There are also 98 species of plants under key protection at the provincial level in Jiangxi Province (first batch in 1994, second batch in 2005).