Red emissive carbon dots (CDs) are highly desired for biological applications. However, serious luminescence quenching of red emissive CDs in aqueous solution greatly hinders their application in high performance biological imaging. Herein, we reported a facile strategy to realize enhanced red emission of CDs in aqueous solution by surface modification with polyetherimide (PEI) via microwave heating method. High photoluminescence quantum yield (PLQY) of 25% was realized from the PEI functionalized CDs (CDs@PEI) in aqueous solution. The proposed PEI functionalization strategy not only protects the red emission against water molecules quenching, but also reverses the surface charges from negativity to positivity to promote cellular uptake of CDs, leading to clear cell imaging in red fluorescence region. More important, CDs@PEI exhibits much better photostability than commercial red emissive dye (MitoTracker red) in cell fluorescent imaging. Potential application of CDs@PEI on fast staining of cells for clonogenic assay has also been demonstrated.