Core-shell (C/S) structured upconversion coated Fe₃O₄ nanoparticles (NPs) are of great interest due to their potential as magnetic resonance imaging (MRI) and upconversion luminescent (UCL) imaging agents, as well as near-infrared activated photodynamic therapy (PDT) platforms. When C/S structured Fe₃O₄@Mn-doped NaYF₄:Yb/Er NPs were prepared previously, well-defined C/S-NPs could not be formed without the doping of Mn during synthesis. Here, the role of Mn doping on the synthesis of core-shell structured magnetic-upconversion nanoparticles (MUCNPs) is investigated in detail. Core-shell-shell nanoparticles (C/S/S-MUCNPs) with Fe₃O₄ as the core, an inert layer of Mn-doped NaYF₄ and an outer shell consisting of Mn-doped NaYF₄:Yb/Er were prepared. To further develop C/S/S-MUCNPs applications in the biological field, amphiphilic poly(maleic anhydride-alt-1-octadecene) (CPMH) modified with amine functionalized methoxy poly(ethylene glycol) (CPMH-mPEG) was used as a capping ligand to modify the surface of C/S/S-MUCNPs to improve biocompatibility. UCL imaging, T₁-weighted MRI ascribed to the Mn ions and T₂-weighted MRI ascribed to the Fe₃O₄ core of C/S/S-MUCNPs were then evaluated. Finally, chlorine e6 (Ce6) was loaded on the C/S/S-MUCNPs and the PDT performance of these NPs was explored. Mn doping is an effective method to control the formation of core-shell structured MUCNPs, which would be potential candidate as multifunctional nanoprobes for future T₁/T₂-weighted MR/UCL imaging and PDT platforms.