This review is different from previous studies focusing on polypyrrole (PPy) in universal fields such as sensors and supercapacitors. It is the first TO systematically review the specific applications of PPy-based electrospun nanofiber composites in the biomedical field, focusing on its biocompatibility regulation mechanism and tissue repair function. Although PPy exhibits exceptional electrical conductivity, redox activity, and biocompatibility, its clinical translation is hindered by processing challenges and poor degradability. These limitations can be significantly mitigated through composite strategies with degradable nanomaterials, enhancing both process compatibility and biofunctionality. Leveraging the morphological similarity between electrospun nanofibers and the natural extracellular matrix (ECM), this work comprehensively analyzes the topological characteristics of three composite fiber architectures—randomly distributed, aligned, and core–shell structures—and elucidates their application mechanisms in nerve regeneration, skin repair, bone mineralization, and myocardial tissue reconstruction (e.g., facilitating oriented cell migration and regulating differentiation through specific signaling pathway activation). The study further highlights critical challenges in the field, including PPy’s poor solubility, limited spinnability, insufficient mechanical strength, and scalability limitations. Future efforts should prioritize the development of multifunctional gradient composites, intelligent dynamic-responsive scaffolds, and standardized biosafety evaluation systems to accelerate the substantive translation of these materials into clinical applications.