The invention discloses phthalocyanine-chitosan oligosaccharide conjugates as well as a preparation method and an application thereof, and belongs to the field of drug preparation. The phthalocyanine-chitosan oligosaccharide conjugates are monosubstituted carboxyl zinc phthalocyanine and chitosan oligosaccharide conjugates or quaternization derivatives of the conjugates, and can be applied to photodynamic bacterial resistance, photodynamic cancer resistance, photodynamic diagnosis and photodynamic disinfection. The phthalocyanine-chitosan oligosaccharide conjugates have double functional groups of phthalocyanine and chitosan oligosaccharide or chitosan oligosaccharide quaternary ammonium salt, thereby being capable of realizing a synergistic treatment effect while realizing photodynamic bacterial resistance; meanwhile, chitosan oligosaccharide has excellent water solubility and biocompatibility, accordingly, amphiphilic property and biocompatibility of phthalocyanine can be improved effectively, toxicity of phthalocyanine can be reduced, and clinical application value of phthalocyanine can be increased.