The rational design of robust fluorescent organic materials for long-term cell tracing is still challenging, and aggregation-caused quenching of emission is a big limitation of this strategy. Organic dyes with aggregation-induced emission (AIE) can effectively address this problem. Herein, AIEgen-containing nanoparticles, with different morphologies and emission, were prepared by assembling amphiphilic copolymers with an AIEgen. We compared the physical and chemical properties of rod-like and spherical nanoparticles, particularly investigating the effects of the shape on internalization and the imaging effect. The formulated nanoparticles exhibit advantageous features, such as a large Stokes shift, robust stability in physiological conditions, strong fluorescent emission, and photobleaching resistance. Interestingly, the rod-like nanoparticles were internalized more efficiently than their spherical counterparts, and their strong green fluorescence can still be clearly observed even after 15 days in vitro and in vivo. This work demonstrates the great potential of regulating the morphology of nanoparticles to obtain an ideal biological function.