Cyclohexene skeletal isomerization was achieved under mild conditions over rationally designed zeolite-based catalysts with high selectivity towards methylcyclopentene and satisfactory stability for multiple runs. The favorable performance was investigated, which can be attributed to unique acidic, structural and morphologic features of optimized Co/NaUZSM-5 catalyst. Further experimental data suggested that carboncationic mechanism might be followed and the reaction mainly occurs within the internal pores of zeolite structures, which was also validated by DFT study.