A dual-template strategy with poly(ethylene glycol) (PEG) and cetyltrimethylammonium bromide (CTAB) was employed to synthesize the β-zeolite nanocrystal aggregates with ultrafine and hierarchical structure (micropores combined with intra-mesopores and inter-mesopores), and the particle size of aggregates and the nanocrystal size of β-zeolites can be systematically tailored by tuning the molar ratios of CTAB/PEG. In the alkylation between benzene and cyclohexene, the β-zeolite nanocrystal aggregates synthesized in the presence of PEG exhibited outstanding activity and resistance to deactivation under harsh reaction conditions, and the lifetime of β-5C4P was extended by 4.3 times compared with the commercial nanosized β-zeolite, indicating that the additional PEG played the role of crystal growth inhibitors to reduce the size of nanocrystals, which increased the amount of accessible external Brønsted acid sites and effectively enhanced the diffusion properties. The experimental data for the spent β-zeolites revealed that the deactivation of zeolites was attributed to the blocking of channels and the loss of active sites occurred due to the inevitable side reactions. In addition, the resultant β-zeolite nanocrystal aggregates also presented robust regeneration performance, which identified a facile and effective route to directly prepare β-zeolite nanocrystal aggregates with excellent catalytic properties in the alkylation of aromatics.