The application of natural antibacterial agents seems to be one of the popular research topics in the field of antibacterial materials due to their unique properties such as good biocompatibility and biodegradability. In this work, 1-ethyl-3-methylimidazolium diethylphosphate ([Emim]DEP) with a better ability to dissolve three natural antibacterial agents (thymol, quercetin, and aloeemodin) was screened out from 195 kinds of ILs formed by 13 cations and 15 anions using the conductor-like screening model for real solvents method. The antibacterial cellulose fibers were prepared using cellulose and three natural antibacterial agents as raw materials and [Emim]DEP as the solvent. The results indicated that three natural antibacterial agents are successfully added into the corresponding antibacterial cellulose fibers according to the Fourier transform infrared, X-ray diffraction, and thermogravimetric analysis data. The scanning electron microscopy results suggested that the antibacterial cellulose fibers have smooth and uniform surfaces. Moreover, the thymol/cellulose antibacterial fibers (TCFs) could inhibit more than 92.3% of E. coli and 90.2% of S. aureus when the content of thymol is 25 wt % and the breaking strength and breaking elongation of the TCFs are up to 580 MPa and 13.8%, respectively. In addition, after 15 times of standard washing in water, the TCFs still have more than 75% antibacterial activities against E. coli and S. aureus.