Phosphorylated cellulose nanocrystal (P-CNC)/imogolite nanotube (natural aluminosilicate nanotube) hybrid thin films were fabricated by spin-assisted layer-by-layer assembly. Phosphorylation of CNC with diammonium hydrogen phosphate ((NH4)2HPO4) was carried out to introduce phosphate groups on the CNC surface for enhanced interaction with imogolite. Structure of the P-CNC/imogolite thin film was characterized by atomic force microscopy, scanning electron microscopy, X-ray diffraction (XRD), and grazing incidence wide-angle XRD. The film thickness increased linearly with the increment of the P-CNC/imogolite bilayer. Benefitting from the strong affinity between the phosphate group of the P-CNC and the Al-OH group of imogolite, the P-CNC/imogolite thin films were quite stable in water within a wide range of pH values, compared with the deterioration of the CNC/imogolite film under same soaking conditions.