This paper reported antibacterial hydroxypropyl chitosan (HPCS)/organic rectorite (OREC)-based nanofibrous mats with intercalated structure fabricated via solution intercalation method and electrospinning. Field emission scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectra, Energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, and inhibition zone surrounding circular mats disks measurement were performed to characterize the morphology, intercalation structure, elements analysis, and the antibacterial properties of the as-spun nanofibrous mats. The results showed that the nanofibrous mats were with better fiber shape with the addition of OREC, the polymer chains were successfully intercalated into the interlayer of OREC, and nanofibrous mats containing HPCS exhibited good antibacterial activities against Gram-negative bacteria Escherichia coli and Gram-positive bacteria Staphylococcus aureus. In addition, the bacterial inhibition ability of the nanofibrous mats was enhanced when OREC was added.