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Knowledge about fertiliser limitation to soil microbes is crucial for exploring microbial community succession and ecosystem functions. In this study, an experiment was conducted to promote ecological restoration by different treatments of organic fertiliser (OF), microbial fertiliser (MF) and non-fertiliser (CK) in a coal mine dump. We investigated microbial community structure using high-throughput sequencing. Soils under OF and MF treatment showed distinct community structures with highly bacterial α-diversity due to the variation of soil pH and organic matters (SOM). Of those, the community dissimilarity between OF and CK was higher. The DistLM analysis indicated that SOM and available nitrogen (AN) significantly influenced microbial community structure. Furthermore, functional annotation by the FAPROTAX revealed that the functional groups associating with C, N, and S cycling increased significantly under OF and MF treatment, but decreased that associated with parasites or symbionts. Compared with MF, the functional groups with OF treatment varied greatly. However, the function groups including nitrogen_fixation, hydrocarbon_degradation and methanotrophy were significantly improved under the MF treatment, which have an important implication for soil quality and microbial growth. It was concluded that MF treatment could improve microbial community structure and enhance potential ecosystem function in coal mine dump soils. [ABSTRACT FROM AUTHOR]