The invention relates to a preparation method of flaky Cu9Fe9S16 nanoflowers. The preparation method includes dispersing a ferric salt and a manganese salt into a solvent with stirring, adding trisodium citrate dihydrate with stirring, adding sodium acetate with mixing uniformly, performing solvothermal reaction for 6-8 hours at 180-240 DEG C prior to centrifuging and washing so as to obtain Fe2MnO4 nanocrystalline; dispersing the Fe2MnO4 nanocrystalline into water, adding a (NH4)2S solution, conducting ultrasonic dispersion and centrifugal washing, and dispersing a product into water so as to obtain dispersion liquid; adding a copper salt solution into the dispersion liquid, and conducting ultrasonic dispersion and centrifugal washing so as to obtain the flaky Cu9Fe9S16 nanoflowers. The preparation method has the advantages of simplicity, safety, environment friendliness, low cost and easiness in operation. The flaky Cu9Fe9S16 nanoflowers are capable of effectively converting near-infrared light into heat and have a nuclear magnetic imaging effect, thereby being quite promising in application prospect for photothermal therapy and diagnosis of cancers.