For the ever-increasing demand for highly safe lithium-ion batteries (LIBs), the common sol-gel process provides heat-resistance to separators with an inorganic coating, where the adhesion to the separator is the key to safety and stability. In this paper, we present a SiO_2.01C_0.23H_x-coated polyethylene (PE) separator through a roll-to-roll atmospheric plasma-enhanced chemical vapor deposition (R2R-APECVD) of hexamethyldisiloxane (HMDSO)/Ar/O₂. The adhesion strength of SiO_2.01C_0.23H_x-coated PE was tested by peel-off test and found to be higher than that of the commercial Al₂O₃-coated separator (0.28 N/mm vs. 0.06 N/mm). Furthermore, the SiO_2.01C_0.23H_x-coated PE separator showed better electrochemical performance in C-rate and long term cycle tests. FTIR, SEM, and XPS analysis indicate that the increased adhesion and electrochemical performance are attributed to the inner hybrid SiO_2.01C_0.23H_x coating with organic and inorganic components.