Abstract: In this paper, the effect of the magnetic field on the optical properties of cellulose nanocrystal (CNC) films with different surface groups was investigated. T-CNC with carboxyl groups on its surface was prepared from cellulose sulfate nanocrystals (S-CNC) by 2,2,6,6-tetramethylpiperidine-1-oxy radical (TEMPO) oxidation. Its basic structure was characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and zeta potential. The effects of magnetic field on CNC films with different surface charges were observed in four modes: no magnetic field, vertical magnetic field, inclined magnetic field, and horizontal magnetic field. The results showed that T-CNC had carboxyl groups on its surface and S-CNC had sulfate groups on its surface. The absolute value of T-CNC potential was lower than that of S-CNC due to the different surface charges. The two kinds of CNC exhibited different self-assembly modes due to the difference in surface charges, in which T-CNC was concentric self-assembly and S-CNC was chiral nematic self-assembly, and the difference in self-assembly modes was not changed by the magnetic field. However, the arrangement of T-CNC and S-CNC in self-assembly process was affected by the magnetic field. With the different orientations of the magnetic field, the color of the two films was affected by the change in the arrangement of CNC. Among them, the vertical magnetic field had the most significant effect on the two kinds of CNC films, which could make the arrangement of CNC in the films more uniform and closer, thus improving the uniformity of film color. The color response of CNC self-assembled films with different surface groups under different magnetic fields lays a foundation for the subsequent regulation of CNC iridescent films and their application in the field of packaging.