As a promising drug nanocarrier, carbon dots (CDs) have exhibited many excellent properties. However, some properties such as bone targeting and crossing the blood–brain barrier (BBB) only apply to a certain CD preparation with limited drug loading capacity. Therefore, it is significant to conjugate distinct CDs to centralize many unique properties on the novel drug nanocarrier. Considering that CDs have abundant and tunable surface functionalities, in this study, a direct conjugation was initiated between two distinct CD models, black CDs (B-CDs) and gel-like CDs (G-CDs) via an amidation reaction. As a result of conjugation at a mass ratio of 5:3 (B-CDs to G-CDs) and a two-step purification process, the conjugate, black-gel CDs (B-G CDs) (5:3) inherited functionalities from both CDs and obtained an enhanced thermostability, aqueous stability, red-shifted photoluminescence (PL) emission, and a figure-eight shape with a width and length of 3 and 6 nm, respectively. In addition, the necessity of high surface primary amine ([sbnd]NH ) content in the CD conjugation was highlighted by replacing G-CDs with other CDs with lower surface [sbnd]NH content. Meanwhile, the carboxyl groups ([sbnd]COOH) on G-CDs were not enough to trigger self-conjugation between G-CDs. Moreover, the drug loading capacity was enhanced by 54.5% from B-CDs to B-G CDs (5:3). Furthermore, when the mass ratio of B-CDs to G-CDs was decreased from 5:30, 5:100 to 5:300, the obtained nanostructures revealed a great potential of CDs as Lego-like building blocks. Also, bioimaging of zebrafish demonstrated that various B-G CDs exhibited properties of both bone targeting and crossing the BBB, which are specific properties of B-CDs and G-CDs, respectively. 2 2