Cumulation of tobacco root secondary metabolite and its effect on the yield and output value were studied on continuous continuous cropping tobacco in Luxi of Honghe as materials，the root secondary metabolite was tested by GC-MS. Taking secondary metabolite on the yield and output value and its relationship were explored by factor analysis and canonical correlation analysis. The results showed that 14 secondary metabolites were detected and determined in the roots of flue-cured tobacco. Through factor analysis，four common factors were extracted，and the cumulative contribution rate reached 85.737%，which were phenolic acid factors，aldehyde ester factors，ester factors and phenolic factors，respectively. Canonical correlation analysis of four common factors and economic benefits of flue-cured tobacco found that the higher the content of 3 substances in flue-cured tobacco roots，such as anisodamine，soft ester acid，arachidic acid，the lower the content of tetradecanoic acid，which was conducive to increasing the yield and output value of flue-cured tobacco，but not conducive to improving the proportion of top-grade tobacco.However，increasing the content of vanillin，dioctyl phthalate and 2，2′-methylene bis-(4-methyl-6-tert-butylphenol)in roots was beneficial to improving the grade structure of tobacco leaves，but not conducive to improving the yield and output value of flue-cured tobacco.Therefore，in order to overcome the obstacles of continuous cropping，it is necessary to carry out relevant technical research to regulate the content of the above seven key secondary metabolites in the root system so as to maintain its balance and improve the yield and output value and grade structure of tobacco leaves.