In this paper, 9 most abundant PBDE congeners in environment and 14 congeners with high/medium biological toxicity were selected as target compounds. Firstly, IR spectra of 23 compounds were divided into 6 spectrum regions based on known vibrational assignment, and their identification abilities for PBDEs were evaluated by using similarity analysis. Then, the spectrum regions with high identification ability relatively have been analyzed to search identification method on the basis of each spectrum characteristic. At last, the principal component analysis and discriminant analysis method were used to extract characteristic spectrum information of congeners with high/medium biological toxicity and establish biological toxicity discriminant model. The triangle breathing vibration region (961～1 153 cm-1) and C—O stretching vibration region (1 153～1 346 cm-1) has been filtered as characteristic IR spectrum regions because of smaller similarity among PBDEs relatively. For the former, the information of vibration peaks distribution can be taken as tool to identification, with the smallest frequency difference of 3.19 cm-1 among 23 congeners and bad ability to distinguish PBDEs from dioxin-similar compounds. For the later, the frequency and shape of main peak is as mark and the smallest frequency difference among PBDEs and between PBDEs with dioxin-similar compounds are 0.74 and 0.67 cm-1 separately, both larger than the common minimum resolution of IR spectrum 0.5 cm-1, depicting good ability for both inner and outer identification of PBDEs. The established biological toxicity discriminant model via discriminant analysis also have shown well ability to biological toxicity prediction, with accuracy of 100% and 88.9% for high/medium and low biological toxicity relatively, representing the extracted IR spectrum information from congeners with high/medium toxicity can realize the accurate classification of biological toxicity for PBDEs.