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Objective: To identify the potential target and mechanisms of hesperidin in MCF-7 estrogen receptor-positive breast cancer cells using bioinformatics approaches. Methods: Gene expression profiles were accessed from public database GSE85871. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was carried out with Database for Annotation, Visualization and Integrated Discovery. The protein-protein interaction network was analyzed by STRING-DB and visualized by Cytoscape. Transcription factor regulatory networks were constructed from TRED, TRRUST, RegNetwork and visualized by Cytoscape. Drug association analysis was conducted by WebGestalt. Results: GO and KEGG pathway enrichment analysis revealed biological processes, cellular components and molecular functions that were related to cancer and estrogen signaling pathways. KEGG pathway enrichment analysis of the genes in transcription factor-differential expression genes regulatory network showed regulation of cancer, estrogen signaling pathways, epidermal growth factor receptor tyrosine kinase inhibitor resistance, and endocrine resistance. Moreover, drug association analysis revealed that hesperidin affected the expression of the same gene as raloxifene. Conclusions: Hesperidin targets estrogen receptor signaling in estrogen receptor-positive breast cancer cells. Results of this study could trace the molecular mechanism of hesperidin in estrogen receptor-positive breast cancer cells and integrative bioinformatics analysis could accelerate drug discovery and development.