SAPO-11 molecular sieves represent one of the most widely studied catalytic supports for alkane hydroisomerization in the petrochemical and coal chemical industries. Herein, we prepared a series of SAPO-11 samples by adjusting the addition amount of the silicon precursor during hydrothermal synthesis. The results demonstrate that the S11-0.25 sample achieves a maximum acid density of 903 µmol g−1 at a SiO2/Al2O3 molar ratio of 0.25. Combined NH3-TPD and 29Si-NMR characterizations confirm that isolated Si sites and minor silicon islands contribute to the enhancement of total acid content and acid strength. Subsequently, the optimized Ni/S11-0.25 catalyst with 4 wt% Ni loading was prepared via impregnation and evaluated for n-dodecane hydroisomerization. This catalyst exhibits excellent isomerization selectivity together with a maximum iso-dodecane yield of 81.1%. The obtained results provide valuable references for the rational design of low-cost non-noble metal hydroisomerization catalysts.