Multimodality molecular imaging has attracted more and more attention recently, as it possesses novel multiple imaging patterns via combining information from several independent molecular imaging techniques. Here, we investigated the multifunctional Mn2+ complex-modified polydopamine (PDA) and dual emissive carbon dots-based nanoparticles (NPs) for trimodality fluorescent, photothermal and magnetic resonance (MR) imaging in vitro and in vivo. In our system, N-doped carbon dots (N-CDs), a kind of green and red emissive CDs, were loaded or embedded onto the PDA NPs for fluorescent imaging. PDA NPs acted as a photothermal agent which showed obvious near-infrared (NIR) absorbance and high photothermal conversion efficiency (28.2%). Moreover, due to the automatic chelation of Mn2+ ions, PDA@N-CDs(Mn) NPs could offer contrast for magnetic resonance (MR) imaging. The application of PDA@N-CDs(Mn) NPs for fluorescent, photothermal, and MR in vivo imaging could be successfully demonstrated. Besides, the cytotoxicity analysis, hemolytic test, histological analysis of viscera sections, as well as blood biochemical analysis have showed that the PDA@N-CDs(Mn) NPs had excellent bio-compatibility and low biological toxicity.