The uncontrolled lithium (Li) dendrite growth significantly impacts the safety performance of polymer separators. To mitigate this growth, this study introduces Si3N4 into sulfonated poly(ether Ether Ketone) (SPEEK) and prepares Si3N4/SPEEK composite separators via electrospinning. At the interface between the Si3N4/SPEEK separator and the Li anode, the Si nanowires that form impede Li dendrite growth, thereby enhancing the electrochemical performance of lithium-ion batteries (LIBs). The Li deposition test of the 10 % Si3N4/SPEEK separator can operate for 1000 h without short-circuiting. Additionally, the LiFePO4||Li cell with the 10 % Si3N4/SPEEK separator shows improved initial discharge capacity (157.8 mAh g−1 at 1C) and superior rate performance (125 mAh g−1 at 10C). Moreover, the nano-scale Si3N4 endows the separator with robust thermal and mechanical properties. The FLIR observations reveal that the 10 % Si3N4/SPEEK separator maintains uniform thermal distribution and structural integrity even at 300 °C, ensuring safe battery operation at high temperatures. The additional load of the 10 % Si3N4/SPEEK separator can reach 10.2 mN, which enhances the puncture resistance of the separator. This work provides a solid approach for the application of SPEEK as a high-safety and high-rate LIB separator.