This study aims to clarify the effects of long-term different fertilization on the soil fertility and grain yield under the continuous maize cropping system in coal mining subsidence areas. The key soil factors were determined in the fertilization treatments for the high maize yield. Four treatments were set with no fertilization (CK), nitrogen, phosphorus and potassium fertilizer (NPK), organic manure alone (M), and organic manure combined with chemical fertilizer (MNPK). Soil samples were also collected in the 0~20 cm thickness. A systematic investigation was made to explore the effects of fertilization treatments on the crop yield, contents of soil organic matter (SOM), total nitrogen (TN), available phosphorus (AP), available potassium (AK), available iron (A-Fe), available manganese (A-Mn), available copper (A-Cu), available zinc (A-Zn), the distribution of aggregates and associated carbon and nitrogen content, as well as the enzyme activities related to carbon cycle. The results showed that the NPK, M and MNPK treatments significantly increased the maize grain yield, especially for M treatment, compared with the CK treatment. M treatment significantly increased the SOM, TN, AK, and A-Mn contents, which increased by 21.50%, 12.50%, 98.37%, and 20.19%, respectively. MNPK treatment was improved the properties of the reclaimed soil. There was the significant increase in the > 2 mm aggregate associated with organic carbon and total nitrogen contents, which were 68.68% and 471.43%, respectively. But the soil A-Cu, and A-Zn contents were reduced by 16.67% and 16.46%, respectively. Moreover, the application of manure (M and MNPK) accelerated the crushing of large macroaggregate (0.25~2 mm), accompanied by the increase of the proportion of silt and clay fraction (< 0.053 mm). In addition, NPK treatment significantly increased the activity of β-glucosidase by 29.17%, but the urease activity was reduced by 29.79%. M and MNPK treatment significantly increased the activities of sucrase, β-glucosidase, urease and alkaline phosphatase, with the increases of 45.87%~73.39%, 54.98%~60.73%, 43.09%~80.32% and 51.52%~54.97%, respectively. Furthermore, the principal component analysis showed that the application of organic manure alone was the better management measure to improve the quality of cultivated land and maintain land productivity in this reclaimed area. The redundant analysis showed that β-glucosidase was a sensitivity index to evaluate the soil fertility, which was contributed 72.40% to the maize grain yield and SOM content. Therefore, the application of organic manure alone can be expected to promote the formation of soil fertility of reclamation under the existing farmland management. The activity of β-glucosidase was enhanced to ultimately improve the crop yield. The effective measure can also be used to maintain the high and stable crop yield for the cultivated land quality in this reclaimed area. The finding can provide a theoretical basis for the improvement of soil and cultivated land quality..