High-performance polymeric separators are indispensable materials for advanced rechargeable lithium-ion batteries (LIBs). In general, separators must simultaneously possess the following qualifications: flame retardancy, mechanical strength, wettability, and ion conductivity. In this paper, a siloxanediamine, namely, 1,3-bis(aminopropyl)tetramethyldisiloxane (APTMDS), is introduced as a means of improving the mechanical properties of the pristine polyimide (PI) separator through hydrolysis-cross-linking. Moreover, dopamine (DA) undergoes self-polymerization to form polydopamine (PDA), which adheres to the surface of the composite separator. This process enhances the compatibility of the separator with the electrolyte. The three-layer composite separator of PI/APTMDS/PDA displays superior wettability, fire resistance, and conductivity in comparison to those of a Celgard-2400 separator. In particular, PI/APTMDS/PDA separators display superior battery capability (128.17 mAh center dot g(-1)@5 C, LiFePO4IILi) in comparison to polypropylene separators (115.4 mAh center dot g(-1)@5 C, LiFePO4IILi). Moreover, the cell employing the PI/APTMDS/PDA separator displays high cycling stability and discharge specific capacity over 100 cycles at 1 and 9 C. The present study offers an excellent design concept for the preparation of modified separators for LIBs.