A functionalized nanocrystal cellulose bearing amino and sulfonic acid groups (Am-sNCC) is prepared through a two-step chemical modification of microcrystal cellulose powders, first by sulfonic acid and then by a 3-trimethoxysilyl propyl ethylenediamine. The structure of Am-sNCC is characterized by Fourier Transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD). A sulfonated poly (ether ether ketone ketone) (Ph-SPEEKK) is synthesized via the direct sulfonation of a high-molecular-weight phenylated polymeric precursor under a mild reaction condition. The nanocomposite membranes composed of the Ph-SPEEKK matrix and the Am-NCC additive are successfully prepared by a solution casting method. The properties related to their application for proton exchange membranes are carefully evaluated. The nanocomposite membranes containing Am-sNCC, which served as a performance-enhancing component to form hydrogen bonding networks with the Ph-SPEEKK matrix, exhibited much improved dimensional stability, higher water absorption capacities, higher proton conductivity, better mechanical and fuel cell properties than the Ph-SPEEKK membrane.