MgAPO-31 molecular sieves substituted by different magnesium contents were synthesized using microwave irradiation (MW) and conventional electrical heating method, respectively. The bifunctional catalysts Pd/MgAPO-31 were prepared by the incipient wetness impregnation technique. The structure and acidity of MgAPO-31 were characterized by XRD, SEM, N2 physical adsorption, FT-IR, and Py-IR. The catalytic performance of Pd/MgAPO-31 were tested in the hydroisomerization of n-decane, which was used as the probe-reaction, and the effect of heating method on acidity of MgAPO-31 and the catalytic performance of Pd/MgAPO-31 were investigated. The results showed that all of the MgAPO-31 samples with ATO topology structure were pure phase and high crystalline materials. The Mg(II) heteroatoms were confirmed to isomorphously substitute for the framework atoms of AlPO4-31 molecular sieve. These Pd/MgAPO-31catalysts showed good catalytic performance for the hydroisomerization in the temperature range of 330–370 °C. The activity of Pd/MgAPO-31 in the hydroisomerization of n-decane and the selectivity for i-decanes were considered to depend on the crystal size and acidity of MgAPO-31.The highest selectivity for i-decanes was obtained over the catalyst Pd/0.05MgA31-MW prepared using the MW method.