Selenium (Se), due to its high electronic conductivity and high energy density, has recently attracted considerable interest as a cathode material for rechargeable Li/Na batteries. However, the poor cycling stability originating from the severe shuttle effect of polyselenides hinders their practical applications. Herein, highly stable Li/Na–Se batteries are developed using ultrathin (≈270 nm, loading of 0.09 mg cm−2) cetrimonium bromide (CTAB)/carbon nanotube (CNT)/Ti3C2Tx MXene hybrid modified polypropylene (PP) (CCNT/MXene/PP) separators. The hybrid separator can immobilize the polyselenides via enhanced Lewis acid–base interactions between CTAB/MXene and polyselenides, which is demonstrated by theoretical calculations and X-ray photoelectron spectroscopy. The incorporation of CNT helps to improve the electrolyte infiltration and facilitate the ionic transport. In situ permeation experiments are conducted for the first time to visually study the behavior of polyselenides, revealing the prohibited shuttle effect and protected Li anode from corrosion with CCNT/MXene/PP separators. As a result, the Li–Se batteries with CCNT/MXene/PP separators deliver an outstanding cycling performance over 500 cycles at 1C with an extremely low capacity decay of 0.05% per cycle. Moreover, the hybrid separators also perform well in Na–Se batteries. This study develops a preferable separator–electrolyte interface and the concept can be applied in other conversion-type battery systems.