Polydopamine nanoparticles (PDA NPs) which combine diagnostic and therapeutic functions are potentially useful in biomedicine. However, it is difficult to synthesize PDA NPs of a relatively small size (≤50 nm in diameter) using the traditional polymerization of dopamine monomers in an alkaline water-ethanol solution at room temperature. Herein, PDA NPs with average diameters ranging from 25 nm to 43 nm are prepared in a way which is similar to the silica-like reverse microemulsion process. The size of the PDA NPs can be modulated by changing the amount of dopamine monomers in the microemulsion. After conjugation with ferric ions (Fe3+), the poly(ethylene glycol) modified Fe-PDA NPs (termed as PEG-Fe-PDA NPs) exhibited pH-activatable magnetic resonance imaging (MRI) contrast and high photothermal performance. The combination of a small dimension and the pH-activatable MRI contrast can greatly facilitate tumor accumulation and increase the tumor imaging sensitivity against animal models in vivo. Completely inhibited tumor growth was achieved by the PEG-Fe-PDA NPs mediated by photothermal therapy with MRI guidance.