Abstract: 【Objectives】 Study of fertilizer effects on growth and development of tobacco mainly focuses on investigating tobacco’s macroscopic indexes (such as agronomic traits, photosynthetic efficiency, and etc.), but how fertilizers affect tobacco cell microstructure in different periods is seldom reported. In this experiment, using cultivar Nicotianatabacum L. K326 as a material, we studied differences of tobacco photosynthesis, leaf gas exchange traits, chlorophyll fluorescence characteristics, chlorophyll content and chloroplast ultrastructure under two different fertilizer treatments, in order to reveal mechanism of fertilizer effects on photosynthesis in both photosynthetic efficiency and chloroplast ultrastructure aspects, and we hope these can provide a theoretical basis for exploring high yield and quality mode in tobacco cultivation.【Methods】 Vermiculite medium was used in pot experiment. Performed the flue-cured tobacco special organic fertilizer(N∶P2O5∶K2O=9∶9∶10,organic matter≥70%,medium and trace elements≥12%)and common urea as the two treatments. Industrialized virus-free tobacco-plants were used for sampling or measurements to which the 6th-8th leaves taking superincumbent phyllotaxis during the leaf age of 15-days, 30-days, 45-days, 60-days and 75-days, and calculating the leaf age from the leaves up to around 2 cm length. The LI-6400 Portable Photosynthesis System (LICOR Inc., Lincoln, Nebraska, USA) was used to measure the net photosynthetic rate, stomatal conductance and transpiration. The Maxi-Imaging-PAM (WALZ, Germany) were used to measure the chlorophyll fluorescence parameters. A spectrophotometer was used to determine the absorbance values of the leaves pigments maceration extract, and calculate the content. The C-7000 Electron Microscope was used for chloroplast ultrastructure observation, the relative ratio of starch granules to chloroplasts (Ra value) was calculated by AutoCAD 2004 (Autodesk, Inc., USA) from digital pictures. Statistical methods of the chloroplast grana lamellae were used according to Teichler-Zallen (improved by Goodenough).【Results】 The results indicate that the organic fertilizer could increase the leaf chlorophyll content and photosynthetic rate, and the effects of the organic fertilizer are improved with the leaf age increasing. At the 60 day of leaves, the leaf chlorophyll content under the organic fertilizer application is 136.1% higher than which under the chemical fertilizer application. At the 75th day, compared to the chemical fertilizer application the photosynthetic rate, conductance and transpiration rate are 135.3%, 84.5% and 51.3% higher, respectively, and the chlorophyll fluorescence parameters, YⅡ and qL, are 22.2% and 39.5% higher than the chemical fertilizer application and the leaf intrinsic photochemical efficiency (Fv/Fm) is 18.7% higher than that at the 60th day, while the non-photochemical quenching (NPQ) is 23.2% lower than the chemical fertilizer application during the 45 day growth stages. Starch grains increase with the leaf age gradually increasing, meanwhile, the area ratio of starch grain to chloroplast (Ra value) is increased. The difference of Ra values between the two different treatments are significant, especially in the 45 leaf-age days, and the leaf Ra value under the chemical fertilizer application is higher than that under the organic fertilizer application (31.8%). Comparing the chloroplast shapes under the two fertilization patterns, the organic fertilizer treatment appears fusiform with a higher aspect ratio, while the chemical fertilizer appears round shape with a lower aspect ratio. 【Conclusions】 The organic fertilizer can significantly increase the tobacco leaf chlorophyll content and photosynthetic rate, and these effects are gradually enhanced with the leaf age increasing. The differences of chlorophyll fluorescence parameters between two different treatments show that the organic fertilization could delay crop senescence and enhance light utilization efficiency of tobacco leaves. The difference of Ra values between two fertilization modes cannot represent if the ability of starch synthesis under the chemical fertilizer application is better. By contrast, the organic fertilization can significantly increase the ratio of chloroplast grana which is the number of lamellae 10 to the total grana lamellae.