Utilizing ionic liquids in proton exchange membranes can greatly enhance the performance of fuel cells, enabling their application in high-temperature and dry conditions. Further advancements in this field depend on a fundamental comprehension of their structural characteristics. This study focuses on the sulfonated poly(ether ether ketone) (SPEEK)-1-butyl-3-methylimidazolium trifluoromethanesulfonate [BMIm][OTf] composite membrane system. Effects of sulfonation degree, ionic liquid content, and temperature on the structure and conductivity of the composite membrane are investigated by dissipative particle dynamics (DPD) and molecular dynamics (MD) simulations. Results show that [BMIm][OTf] is predominantly distributed around the sulfonic acid groups of SPEEK. At an optimal sulfonation degree and ionic liquid content, interconnected ionic liquid channels can be formed. Nevertheless, an excessively high sulfonation degree may jeopardize the stability of the membrane structure. Moreover, the aggregation of ionic liquid occurs at a high level of ionic liquid content, which hinders the efficient transfer of protons. Generally, increasing the temperature is more conducive to the formation of monodisperse ionic liquid channels within the SPEEK-[BMIm][OTf] composite membrane; however, overhigh temperature may compromise the integrity of the composite membrane structure. The findings of this study offer molecular insights for the development of high-temperature proton exchange membrane fuel cell systems.