As a primarily way to protect biodiversity, building nature reserves has received attention in all countries of the world. Evaluation of the value of biodiversity protection in nature reserves and their management. have become an important project. In order to evaluate the value of biodiversity protection among national nature reserves in Northeast China, we selected 40 national nature reserves and evaluated the species biodiversity protected value (SBPV) and Germplasm genetic biodiversity protected value (GGBPV) of the protected animals and plants in these national nature reserves. Threatened categories, endemism, and protection level indexes were used to evaluate SBPV, while taxonomic distinctiveness, threatened categories, and relative degree indexes were used to evaluate GGBPV. The comprehensive species protection value (CSPV) was determined by standardizing the SBPV and the GGBPV of the nature reserves. The results showed significant differences in the value of biodiversity protection among different nature reserves, and that there were small differences between the wild animal GGBPV and the plant GGBPV in same nature reserves, while the plant GGBPV being significantly higher than the animal GGBPV in most nature reserves. There were large differences in the CSPV among these nature reserves though they are all national nature reserves. The CSPV was higher in Jilin Changbai mountain national nature reserve, Jilin Hunchun amur tiger national nature reserve, and Jilin Songhua river national nature reserve than in the other nature reserves, and was lower in Liaoning Zhanggutai nature reserve, Heilongjiang two-river nature reserve, and Heilongjiang Sanjiang-Huanpao nature reserve. Considering that different kinds of nature reserves showed significant differences in their CSPV, the evaluation method used in this study was not affected by the differences in the types of nature reserves. This research showed that:our method can be used to evaluate the species protected value of nature reserves successfully, and that the results can be compared with each other; this method would not cause biasness due to differences between the habitats and species distribution; and that this method needs to be improved in terms of GGBPV calculation. The results of this study can be used as an important reference to study the management of nature reserves in northeast China. Evaluating the biodiversity protected value and assessing its rank is helpful to reduce the subjectivity.