With the increasingly strict environmental protection requirements and the continuous improvement for the performance of clean fuel, it is imperative to develop technology for producing high octane gasoline blending components. Alkane isomerization was one of the important ways due to it contain little olefin and aromatic components which are harmful to the environment. In this study, the multistage porous composite NixPy-MCM-41/MOR catalysts were synthesized in the hydrogen atmosphere, the conversion rate and selectivity of n-hexane hydrogen isomerization with different conditions was tested in a fixed bed reactor. The results shown that the loading volume of active components is 4.0 wt%, nickel-phosphorus ratio of 0.5, reaction temperature of 250 °C, reaction pressure 3.0 MPa and volume space velocity is 2.0 h−1 with the hydrogen condition showed good catalytic activity for the n-hexane isomerization. The conversion rate of n-hexane is 73.0 % and the selectivity of 84.0 %, respectively. The isomerization stability of the Ni2P-MCM-41/MOR catalyst was investigated. After the long period test, the catalytic activity of the catalyst could keep good. Based on the study of reaction effect with different test conditions in hydrogen atmosphere, the mechanism of alkane isomerization for Ni2P-MCM-41/MOR catalyst was proposed.