Herein, small-sized fluorescent carbon nanoparticles (CNs) with tunable shapes ranging from spheres to various rods with aspect ratios (ARs) of 1.00, 1.51, 1.89, and 2.85 are prepared using a simple anion-directed strategy for the first time. Based on comprehensive morphological and structural characteristics of CNs, along with theoretical calculations of density functional theory and molecular dynamics simulations, their shape-control mechanism is attributed to interionic interactions-induced self-assembly, followed by carbonization. The endoplasmic reticulum-targeting accuracy of CNs is gradually enhanced as their shape changes from spherical to higher-AR rods, accompanied by a Pearson's correlation coefficient up to 0.90. This work presents a facile approach to control the shape of CNs and reveals the relationship between the shape and organelle-targeting abilities of CNs, thereby providing a novel idea to synthesize CNs that serve as precise organelle-targeted fluorescent probes.