The photostability, photodestructive efficacy, two-photon excitation cross section, and two-photon fluorescence of gold nanoparticles conjugated with a hydrophilic photosensitizer, indocyanine green, via multiphoton laser exhibited an increased size effect in methicillin-resistant Staphylococcus aureus and A549 cancer cells that was dependent on the size of multifunctional gold nanomaterials, but the effect only occurred when nanomaterials within 100 nm in diameter were used. Besides, the enhanced effectiveness of photodestruction, photostability, and contrast probe indicated an additive effect in the therapeutic and imaging efficiency of multifunctional gold nanomaterials. Consequently, the preparation of the multifunctional gold nanomaterials and their use in biomedical applications via multiphoton laser is an alternative and potential therapeutic approach for killing bacteria and for ablating cancer cells.