Ecochemometrics is an effective method to study the balance of ecosystem and multiple chemical elements, and to clarify the impact of different fertilization systems on the carbon, nitrogen, phosphorus content and their ecostoichiometric ratio of plant-soil-microbial continuum, which can provide a feasible basis for revealing the nutrient cycle of ecosystem and realizing the element balance and sustainable development of mining reclamation agricultural system. In this study, the reclaimed land of the waste dump of Wujiata open-pit coal mine was taken as the research object, and six fertilization treatments were set up, including single application of organic fertilizer with three green manure ratios (A1B0, A2B0, A3B0) and microbial inoculum with different organic fertilizers (A1B1, A2B1, A3B1). The characteristics of carbon, nitrogen and phosphorus of plant-soil-microbial ecosystem were studied in combination with the planting of Sophora flavescens. The results showed that:(1) Compared with the single application of organic fertilizer, the combination of organic fertilizer and microbial inoculum had a significant effect on stem and leaf phosphorus, soil carbon, nitrogen, phosphorus and microbial biomass nitrogen (p<0.05), but had no significant effect on root nutrient. Among them, the combination of microbial inoculum and A1 organic fertilizer had the greatest impact on soil total phosphorus, increasing by 90.06%. Under the combination application of A2 organic fertilizer, the soil organic carbon and biomass nitrogen were affected most obviously, increasing by 104.60% and 71.95%, respectively. Under the combination application of A3 organic fertilizer, the total phosphorus in stem and leaf and soil total nitrogen were significantly affected. The total phosphorus in stem and leaf decreased by 183.96%, while soil total nitrogen increased by 29.14%. (2) Under the fertilization treatment, compared to the stem and leaf and microorganisms, the internal stability of S. flavescens root was weaker and more sensitive to exogenous nutrient inputs. (3) Under fertilization treatment, there was a strong coupling relationship between plant root nutrients and soil and soil microorganisms, so the nutrient balance of each component could be coordinated through root sensitivity to maintain plant stability.