Among the most selective catalytic systems for the hydroisomerization of C16+ n-paraffins, catalytic systems based on SAPO-11 are quite promising. In order to increase the activity and selectivity of these bifunctional catalysts, it is necessary to reduce the diffusion restrictions for the reacting molecules and their products in the microporous structure of SAPO-11 by reducing the crystal size. To solve this problem, we have studied the influence of different templates (diethylamine, dipropylamine, diisopropylamine, and dibutylamine) on the physicochemical properties of reaction gels and SAPO-11 silicoaluminophosphates during their crystallization. Using XRD, SEM, and NMR techniques, we found that regardless of the template used, the reaction gel after the aging process at 90 °C is an AlPO4·2H2O hydroaluminophosphate. At the same time, the nature of the template affects the morphology and crystal sizes of the intermediate alumophosphate, AlPO4·2H2O, and the molecular sieves, SAPO-11. The acidic properties and the porous structure characteristics of SAPO-11 are also affected by the template. A template was proposed to enable the synthesis of nanoscale SAPO-11 crystals. The influence of the morphology and crystal size of SAPO-11 on the catalytic properties of a bifunctional catalyst based on SAPO-11 in the hydroisomerization of hexadecane was investigated.