Abstract: Aiming at the diseases that appear in gene editing tobacoo materials, based on the differential analysis, we developed a high-throughput FTIR primary screening method based on the characteristics of tobacco material diseases as the core of research. Based on the premature flowering and normal seedling formation period study, showed that tobacco leaf carbohydrates increased significantly after premature flowering, while the protein content did not change significantly, ratio of sugar to protein increased significantly. The carbohydrates may be premature flowering tobacco plants flowering signal factor. Study on the chlorisis leaves and normal leaves showed that the carbohydrate in chlorisis leaf decreased significantly, and the protein content was basically unchanged. While the nitrate was enriched in chlorisis leaves, which may be due the photosynthesis decreased in chlorisis leaves, the absorption and assimilation of plant nitrate were decreased, but the assimilation decreased more significantly, therefore, the nitrate was enriched in chlorisis leaves. It is also possible to block or reduce the assimilation of nitrate in plants due to the editing of gene loci. The enrichment of nitrate in tobacco leaves can be used as a preliminary screening criterion for this type of chlorisis disease, and the characteristic peaks of the chlorisis tobacco were in 1384 cm-1 and 829 cm-1. In addition, the changes in the chemical composition are verified by other analytical methods and the results are consistent. The principal component analysis showed that the disease tobacco could be distinctly distinguished from the control tobacco, and a preliminary determination model of the related diseases tobacco was established. The results showed that the analysis results of FTIR technology had high accuracy, and the difference between them was obvious. It could be applied to high-throughput primary screening for early disease diagnosis and disease analysis of gene editing tobacco materials.