Ru(bpy)3@SiO2-COOH and Ru(bpy)3@SiO2@CD47-peptide nanoparticles (NPs) with fluorescent and mass spectrometric properties were designed and synthesized as the models of drug-nanocarriers. Their phagocytic internalization could be quantitatively measured using more sensitive inductively coupled plasma mass spectrometry (ICPMS) (102Ru) versus traditional laser confocal scanning microscope (λex/em = 458/600 nm) for the first time. Modification of a self-signal trigging CD47-peptide on the NPs' surface decreased internalization by 10 times, (2.79 ± 0.21) × 104 Ru(bpy)3@SiO2-COOH and (0.28 ± 0.04) × 104 Ru(bpy)3@SiO2@CD47-peptide NPs per RAW264.7 macrophage (n = 5). The alkynyl-linked CD47-peptide allowed us to quantify the number (2412 ± 250) of CD47-peptide modified on the NP and the total content (5.14 ± 0.25 amol) of signal regulatory protein α (SIRPα) on the macrophage by measuring the clickable tagged Eu using ICPMS. Furthermore, the interaction between CD47-peptide and SIRPα as well as the changes of the remaining free SIRPα during the internalization process of Ru(bpy)3@SiO2@CD47-peptide NPs were quantitatively evaluated, providing direct experimental evidence of the longspeculated crucial CD47-SIRPα interaction for drug-nanocarriers to escape internalization by phagocytic cells. Remarkable difference in the internalization ratio of 12.3 ± 4.8 of Ru(bpy)3@SiO2-COOH NPs and 4.3 ± 0.5 Ru(bpy)3@SiO2@CD47-peptide NPs with and without the protein corona indicated that CD47-peptide still worked when the protein corona formed. Not limited to the evaluation of the NPs studied here, such a fluorescent and mass spectrometric approach is very much expected to apply to the assessment of other drug-nanocarriers designed by chemists and before their medical applications. Graphical abstract.