Strengthened poly(lactic acid) (PLA)-based materials with improved mechanical performance and improved thermal resistance, notably, are prepared by introducing stereocomplex crystallite (SC), an ideal filler, into the materials. Owing to the intermolecular hydrogen bond among the stereoisomer chains, the melting point of the special crystallite is up to 200 °C, which is 50 °C higher than the isostatic crystallite. The modulus of the PLA-based materials can be enhanced to several 100 MPa because of the integrated polymer chain arrangement. In this study, we electrospun hybrid nanofibers consisted of PLA stereoisomers and induced the stereocomplex crystallization under a mild condition (65 °C for 1 h). The mild warming is favorable for the protection of chlorogenic acid (CA) that was selected as the antibacterial agent. Both of Gram-positive and Gram-negative bacteria were efficiently cleared away using the warmed nanofibers that released CA rapidly within just a few hours. Used as filters, the SC electrospinning membrane also presented a potent filtering effect, leaving no bacteria retained in the filtrates. Attributing to SC, the PLA-based nanofibers showed extremely increased melting temperature over 200 °C and improved Young's modulus up to 270.0 MPa. The durable nanofibers prepared in present study are meaningful for enlarging the application of PLA-based materials, for example, as filters, masks, and packages.