In this study, the chlorophyll fluorescence analysis was used as a technical means to study the effects of PAHs (Phe) stress in soil on chlorophyll fluorescence characteristics and light energy distribution parameters of Glycine soja. The results showed that Phe stresses can decrease PSⅡ activity center and the electron transfer ability, resulting in the decrease of the light energy utilization ability, especially for the use of the strong specular ability. Under 200 mg·kg^-1 Phe stress conditions, F_v/F_m, q_P, ENR and NPQ were changed, and slow light inhibition occurred in G. soja leaves, which reduced the electron transport capacity and photosynthetic reactivity of the photosynthetic electron transport chain. Under the control of different light intensity and the increase of concentration of Phe stresses that G. soja leaves chlorophyll fluorescence response curve Ф_PSⅡ and q_P parameters showed a trend of decrease, increase of NPQ launched the PSⅡ cycles way excitation energy dissipation of excess radiation, in order to maintain the normal physiological function of photosynthetic institutions. Those parameters such as F_m, F_v/F_m, F_v/F_o and PI_ABS decreased with the increasing concentration of Phe, which means that the soils Phe stressing subdued the photochemical activity of PSⅡ of those G. soja. Based on the study of electronic supply and transmission capacity at electronic donor side and receptor side of the PSⅡ found that on 0.3 ms (K point) of the OJIP curve of Phe stressed G. soja leaf, the fluorescence intensity increased the activity of OEC decreased. Phe stressing also caused the increase of the fluorescence intensityat the J point and I point on the OJIP curve of Phe stressedG. soja leaf. It showed that the Phe stressing reduced the electronically acceptability at the electronic receptor side of PSⅡon the leaves of G. soja, and made the electronic from Q_A to Q_B transfer blocked. The optical energy absorption and distribution parameters of seedling leaves of G. soja were influenced by Phe stressing. With the increase of soil Phe concentration, theratio of optical energy absorbed by PSⅡ reaction center and used for electron transfer after Q^-_A and the energy absorbed by each unit reaction center and used for electron transfer was reduced in the leaves of treated G. soja. It means that the proportion of optical energy captured by the reaction center and used for the photochemical reaction was reduced, and the proportion used through the invalid heat dissipation was increased. It could be concluded that there were three important reasons that generated the reduction of activity of PSⅡ reactive center of G. soja leaves under the soil Phe stress, which was the damage of OEC at electron donor side of PSⅡ, the electron transfer ability reducing at the electron acceptor side of PSⅡ and the change of the distribution and utilization of optical energy. This studise on the chlorophyll fluorescence analysis technique could provide guidance for the effect mechanism of plant photosynthesis to PAHs (Phe) stress.