Herein, an Al-containing MFI zeolite subcrystal (Al-MFI-SC) with a size less than 7 nm and extracted from the synthetic system of ZSM-5 zeolites was employed as an acidic support to disperse metal nickel (Ni) species. Various characterization results confirmed its ultrasmall size, large external surface area, uniformly accumulated mesoporous structure, and abundant weak acidity. Different from Ni species supported on nano and commercial HZSM-5 zeolites, Ni nanoparticles, similar in size to Al-MFI-SC, were discretely embedded in the Al-MFI-SC support, achieving a stable high dispersion of Ni species in it. As a result, the prepared Ni-embedded zeolite subcrystal (Ni/Al-MFI-SC) catalyst exhibited surprisingly high activity in the hydrodesulfurization (HDS) of 4,6-dimethyl-dibenzothiophene. The turnover frequency (TOF) of its desulfurization was 6.2 and 10.1 times higher than that of Ni species supported on nano and commercial HZSM-5 zeolites, respectively, which is attributed to its high dispersed Ni species, abundant accessible acidic sites and unique micro–mesoporous structure. Moreover, this Ni/Al-MFI-SC catalyst displayed a high desulfurization performance in the presence of metalloporphyrin compounds and high reaction stability, which can be attributed to the large external surface area of the zeolite subcrystal carrier and stable HDS ability of Ni species. This study demonstrates the significance of zeolite subcrystals with ultrasmall size, appropriate acidity, and short diffusion channels as ideal catalysts and metal carriers for bulk molecule conversion.