Silicalite-1-type zeolites with unique intracrystal holes or cracks were successfully prepared using a cellulose nanofiber (CNF) as an additional mediating material, and their vapor phase adsorption properties toward methyl tert-butyl ether (MTBE) and n-nitrosodimethylamine (NDMA) were examined. It was found that the mixing protocol of CNF and structure-directing agents (SDAs), the addition amount of CNF, and the CNF/SDAs amount ratio play important roles in forming the holed silicalite-1. The synthesis route that preliminarily mixes CNF with SDAs in a series of controlled conditions is particularly beneficial for the formation of the holed silicalite-1 with mesoporosity and larger pores because the CNF-SDAs composite structure benefits the zeolite growth closely encompassing CNF inside the crystal structure. It also promotes the preferential formation of the orthorhombic phase vicinal to the CNF surface, namely, the surface of the formed internal holes or cracks, with the twin-type crystal size reduced as compared to the non-CNF-templated sample. On the contrary, the synthesis route that mixes CNF with SDAs–silicate composite ions tends to modify the twin-type crystal shape at the same time to form small but uniform well-crystallized particles with less holes or cracks and a dominative monoclinic phase. It was considered that both the inter-subunit structural defect and silanol defect whose content is increased with CNF addition influence the adsorptivity of MTBE and NDMA. Owing to the small twin-type crystal size, the smaller crystal subunits, and the favored short path from the surface of internal holes or cracks, the holed silicalite-1 derived from the CNF and SDA premixture assures the easiest access of adsorbate molecules to the most energetically favored sites and is most appropriate for the adsorption of both MTBE and NDMA among the examined zeolites.