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With constant emergencies and severe consequences of various central nervous system (CNS)-related diseases, drug delivery gradually reveals its significance in the modern medicine. The biggest challenge of drug delivery resides in the selection of appropriate drug delivery carrier. 21^th century witnessed the prosperous development of diverse nanomaterials. Due to many excellent properties revealed in nanoscale, nanomaterials have been widely investigated as drug nanocarriers. As a new family member of carbon-based nanomaterials, carbon dots (CDs) have proved to be promising drug nanocarriers. They have been successfully conjugated with various therapeutic agents for targeted drug delivery. However, considering the limitation of single CD preparation in drug delivery, in this study, two distinct CD preparations (G-CDs and Y-CDs) were conjugated to compensate for each other’s deficiencies. Different dialysis bags were employed to purify the CD conjugate (G-Y CDs) and reveal the difference between small and large-conjugated systems. After a series of physicochemical characterizations, G-Y CDs exhibited many nanocarrier-favored properties such as excitation-dependent photoluminescence (PL), diversified surface functionality, controlled morphology and versatile amphiphilicity. To further analyze the formation mechanism of G-Y CDs, self-conjugation was separately surveyed with G-CDs and Y-CDs, which showed that self-conjugation was able to occur between Y-CDs. Eventually, to evaluate the capacity of G-Y CDs as drug nanocarriers for future CNS-related diseases, G-Y CDs were intravascularly injected into the heart of zebrafish. The fluorescence signal in the spinal cord suggested the capability of G-Y CDs to cross the blood-brain barrier (BBB). Therefore, this study reveals a novel strategy to assemble versatile drug nanocarriers through conjugation of distinct CDs.