Aberrant amplification of the human epidermal growth factor receptor 2 (HER2) genes can lead to excessive proliferation of cancer cells and tumor progression. When conventional optical microscopy is used to detect the HER2 gene in breast cancer cells with high amplification levels, the fluorescent spots of the fluorescence in situ hybridization (FISH) probe tend to appear as clusters, making accurate counting challenging. In this paper, structured-light illumination super-resolution microscopy is applied to image pathological sections of HER2 gene fluorescence in situ hybridization, in order to resolve fluorescent probes close to each other. Through large field scanning imaging and image stitching, hundreds of cells can be imaged with super-resolution and statistically analyzed. The proposed method allows more accurate enumeration of aggregated fluorescent spots on slides with high-level gene amplification.