Background: Enzyme activities play a very important role in metabolism. Carbon (C) and nitrogen (N) are the two most basic elements for plant growth and development, and their mutual coupling makes C:N become an important index to explore plant element allocation and adaptation strategies. Although the key enzymes activity in carbon and nitrogen metabolism, and defense enzymes are often used to indexes of the physiological and biochemical characteristics of plants, the relationship between them and biomass still lacks understanding. In this paper, under the control condition, the biomass and 18 kinds of physiological and biochemical indexes were obtained through 24 groups experiments of the regenerated seedlings of Salvia miltiorrhiza by 9 endophytic fungi strains grafted. Results: The data were analyzed by descriptive statistical analysis, Lasso variable screening analysis and MLP neural network regression analysis. Results show that many physiological and biochemical indexes are related to biomass, and glutamine synthetase ( GS ),glutamate synthase ( GLS ), glutamate dehydroge nase ( GDH ), peroxidases (POD), catalase (CAT), soluble protein are the key factors which affect the biomass synthesis of Salvia miltiorrhiza . Conclusion: In this paper, it discusses the relationship between physiological and biochemical indexes and biomass in a comprehensive and systematic way by the framework of "Build-Design-Calculate-Test". Through rigorous logical reasoning process, the factors affecting the growth of Salvia miltiorrhiza are selected, and the mathematical model is established. It also provides a powerful tool for the comprehensive and systematic study of plant growth and the synthesis of effective components.