The tailored synthesis of plate-like SAPO-11 molecular sieve was achieved by introducing seed-surfactant directing agent into the synthesis system for the first time. The effects of morphological change of SAPO-11 molecular sieve on the physicochemical properties of SAPO-11 and the active phase properties of the catalyst were analyzed via a series of characterization techniques. The hydroisomerization of n-hexadecane was used as the model reaction to evaluate the catalytic performance of NiWS supported catalysts based on SAPO-11 molecular sieve with different morphologies. The plate-like SAPO-11 possessed better textural properties and acidity than pseudo-spherical SAPO-11. Meanwhile, the stacking number, dispersion and metal sulfidation degree of the active phase of sulfided NiW/SAPO-11-P were improved, and its high proportion of type II active phase optimized the metal–acid synergistic catalytic mechanism. Through tracking and analyzing the crystallization process of plate-like SAPO-11, the formation mechanism of plate-like SAPO-11 was investigated and revealed. The adsorption kinetics, diffusion behavior and catalytic kinetics of n-hexadecane on the catalysts were emphatically investigated. The optimized support structure and active phase properties improved the intrinsic catalytic activity and hydroisomerization reaction path priority of NiW/SAPO-11-P. It was found that the hydroisomerization reaction on NiW/SAPO-11-P was carried out under the reaction-limiting conditions, while the hydroisomerization reaction on NiW/SAPO-11-C was carried out under the reaction-controlling conditions. The effects of plate-like SAPO-11 on the activity stability of the catalyst was investigated, and the essential reasons for the differences in activity stability of the catalysts were revealed through comprehensively analyzing the coke formation difference and diffusion behavior difference. It is expected to provide reference for the tailored design of SAPO-11 molecular sieve with special morphology and the preparation of efficient hydroisomerization catalyst.