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Graphene quantum dots (GQDs) have good biocompatibility, high luminescence, and low photobleaching properties, which make them promising alternatives to fluorescent dyes for cell imaging. However, most of the reported GQDs lack targeted selectivity that limits their applications in biomedicine. To overcome the drawback, novel GQDs modified with polyethyleneimine (PEI) or (3-carboxyl) phenyl bromide phosphine (TPP) were originally synthesized via a facile, low-cost, environmentally friendly, and large-scale preparation method. The GQDs-PEI was synthesized by a simple hydrothermal process, and then TPP was conjugated to the GQDs-PEI via the amide linkage. The physicochemical, optical, biocompatible, and targeted imaging properties were evaluated systematically. The results indicated that the average sizes of the as-produced GQDs-PEI and GQDs-TPP were 3.75 and 3.25 nm, respectively. More significantly, the two composites had excellent optical property, low cytotoxicity and selective targeting and imaging properties for cell nucleus or mitochondria, suggesting their promising applications as the cell nucleus imaging or mitochondria imaging in vivo and in vitro for diagnosis and therapy of some related diseases. • GQDs were originally synthesized via a facile, low-cost, and large-scale method. • The synthesized GQDs had excellent optical property and low cytotoxicity. • The synthesized GQDs can selectively target and image the nucleus and mitochondria. • The imaging properties of GQDs were comparable to the commercial fluorescent dyes. [ABSTRACT FROM AUTHOR]