Nanozinc oxide (ZnO) is a known material for its high therapeutic efficacy against citrus canker. However, the influence of particle size on the antibacterial activity of nano-ZnO against Xanthomonas citri subsp. citri (Xcc), as well as the distinct bacterial response mechanisms to different nanoparticle sizes, remain poorly understood, limiting its broader application. In this study, differences in the antibacterial potentials of nano-ZnO particles with sizes of 30, 90, and 200 nm against Xcc were investigated. The results showed that the zeta potential of the three nano-ZnO variants displayed no significant differences. However, the antibacterial efficacy of nano-ZnO against Xcc was strongly dependent on particle size, with smaller particles exhibiting greater antibacterial activity. This is attributed to their increased capacity to damage bacterial cell membranes and DNA, which is linked to a higher generation of reactive oxygen species and greater release of Zn2+ within the bacterial cells. In addition, small-sized nano-ZnO exhibits superior efficacy in inhibiting biofilm formation, exopolysaccharide secretion, and xanthomonadin production in Xcc. Fourier transform infrared multivariate and two-dimensional correlation analyses revealed that macromolecular components in Xcc exhibited more pronounced responses to smaller-sized nano-ZnO particles, further supporting their superior antibacterial efficacy. In conclusion, this study provides valuable insights into the size-dependent antibacterial mechanisms of nanomaterials and offers a theoretical basis for the effective application of nano-ZnO in the control of citrus canker.