Aiming at the problems of non-intuitive geological information and difficult multi-source data fusion in coal mines, this paper takes Yinxing No.1 Mine as an example to carry out three-dimensional geological modeling and application research based on multi-source data fusion. By integrating multi-source geological data such as drilling, geophysical exploration and geological realism, the spatial fusion and unified correction of data are realized by using multi-source data fusion technology, which provides a reliable data basis for modeling. On this basis, a three-dimensional comprehensive geological model of mine including roadway engineering, key coal seam, stratum structure and hydrogeology is constructed, and the three-dimensional visualization of geological structure and production scene is realized. The model supports arbitrary cutting analysis, and can automatically generate geological section and coal seam floor contour and thickness contour map, which can clearly reveal the spatial fluctuation and thickness variation law of coal seam. At the same time, the model is applied to the geological navigation of the mining face, which can dynamically generate the fluctuation curve of the coal seam and the change curve of the coal thickness, which provides a precise geological basis for the layout of the working face and the safe mining. The research results have improved the level of mine geological transparency and digitization, and provided effective technical support for safe and efficient mining of coal mines under complex geological conditions.