In order to discuss the feasibility of chemical composition of complete tobacco by near infrared spectroscopy analysis technique, we used near infrared spectroscopy analysis technique to study spectrum acquisition of the complete flue-cured tobacco leaves and total alkaloid quantitative analysis modeling methods. The samples of the flue-cured tobacco in this research were collected from different towns and different varieties in Kunming city of Yunnan province. Respectively with tobacco leaf tip, the middle part of leaf, leaf base spectrum and the three parts of the average spectrum to establish quantitative analysis model for total alkaloids of flue-cured complete tobacco leaves with Partial Least Squares (PLS); respectively use KS and SPXY methods to divide flue-cured tobacco samples into calibration set and validation set and use back interval partial least squares (BiPLS), no information on variable elimination method (UVE) and competition adaptive re-weighted sampling method (CARS) to select characteristic variables to optimize the model. Research results showed that, the prediction accuracy of the model established with tobacco leaf tip, the middle part of leaf, leaf base spectrum the three parts of the average spectrum improves 8.5%~9.5% compared to the model established with the spectra of the individual parts. Compared with full-spectrum modeling, using KS-BiPLS to establish the model can significantly improve the model’s predictive ability and the prediction accuracy of the model is improved by about 10%. The correction coefficient and root mean square error of the model are 0.917 4 and 0.226 1 respectively. The determination coefficient and root mean square error of the validation set are 0.902 0 and 0.200 7 respectively. This method is applied to flue-cured complete tobacco leaves and it can be used to estimate total alkaloids of flue-cured complete tobacco leaves content rapidly and non-destructive. It will save a lot of time for a large number of flue-cured tobaccos. And it will also help to provide technical support for the classification of the flue-cured tobacco leaves and improve the quality of raw materials and provide scientific basis for the process control of cigarette production.