A quantitative detection method of rare earth doped calcium phosphate fluorescent nanoparticles (RE-nCaP) in organisms includes establishing a fluorescent intensity-concentration standard curve of rare earth ions, preparing samples to be tested and the blank control group into homogenate, performing centrifuging and testing the fluorescent intensity of supernatants, calculating the fluorescent intensity values per unit mass or volume of the samples and the blank control group, and performing significant difference analysis; if P is greater than or equal to 0.05, determining that the RE-nCaP content in the samples is 0, and if P is smaller than 0.05, testing the tissue extraction rate of RE-nCaP; and comprehensively considering the tissue extraction rate, the homogenate volume, the fluorescent intensity value per until mass or volume, the homogenate dilution ratio, and the doping amount to obtain the accurate content of the RE-nCaP in biological tissue samples.