In this article, a bifunctional polymer (PEG-NHCH2COOH) with amino group and carboxyl group was synthesized by nucleophilic substitution of methoxy polyethylene glycol tosylate (PEG-OTs) and methyl N-acetylglycinate, and hydrolysis reaction. Next, the hydrophobic fluorescent dye borondipyrromethene (BODIPY) was conjugated with the bifunctional polymer (PEG-NHCH2COOH) by C-N covalent bonds resulting a new fluorescent polyethylene glycol amino acid derivative (B-BODIPY). After, B-BODIPY was coordinated with the Mn(II) ion, multifunctional borondipyrromethene polyethylene glycol manganese(II) nano-particles (G2MnNPs) was formed through microemulsion self-assembly method. The nano-particles (G2MnNPs) were characterized by infrared spectroscopy (FT-IR), UV-vis and TEM testing methods. Cell imaging and mitochondria imaging experiments showed that the G2MnNPs was a low toxic multifunctional tumor imaging agent including mitochondrial targeting, fluorescence imaging and magnetic resonance imaging in cancer cells.