Selective synthesis of nanocluster (NC) isomers with tailored structures holds significant importance for enhancing their applications. Here, we develop an effective strategy for the selective synthesis of CdS NC isomers through the judicious choice of a pair of carboxylic acid isomer additives. Specifically, CdS NC-312 and NC-323 (denoted by their UV-vis absorption peak position) could be selectively produced by introducing a conventional mixture of Cd and S precursors, with the addition of 2-methylbutyric acid (2-MA) and 3-methylbutyric acid (3-MA), respectively. The synthesized NC isomers demonstrated a precise isomeric relationship, sharing both the isomeric inorganic core and organic surface. Alternatively, the as-synthesized NCs were interconvertible by re-adding the acid isomers. The density functional theory calculations further support that 2-MA and 3-MA have specific selectivity for producing CdS NC isomers by interfacial tuning. Finally, the generality of this methodology was also evidenced with applications in other CdS NC synthetic systems. This study unveils the intriguing correlation between additive structures and the configuration of NCs, providing a foundation for the selective synthesis of NC isomers.|Here, we develop an effective strategy for the selective synthesis of CdS nanocluster isomers through the judicious choice of a pair of carboxylic acid isomer additives.