Precise control of heterogeneous nucleation at inorganic interfaces is essential for constructing uniform multicomponent nanostructures but remains challenging because nucleation is highly sensitive to local surface chemistry. Here, we demonstrate a ligand-programmed interfacial nucleation strategy for controlling ferrite-gold growth through regulation of surface citrate coverage. Using gold magnetic nanoparticles (GMNPs) composed of Fe₃O₄ and Au as a model system, we show that surface-bound citrate modulates gold precursor adsorption and the heterogeneous nucleation landscape, enabling interlayer-free aqueous synthesis of highly uniform nanostructures with tunable sizes. Notably, citrate transforms iterative gold deposition from a heterogeneity-amplifying process into a self-homogenizing process by suppressing secondary nucleation and excessive growth of pre-existing particles while promoting utilization of residual ferrite nanoparticles. Surface citrate quantification and density functional theory calculations reveal that increasing citrate coverage strengthens interfacial Au-O electronic coupling, charge redistribution, and gold precursor adsorption, providing a molecular basis for the observed growth behavior. The strategy is further validated in Co_0.5Fe_2.5O₄@Au and Mn_0.5Fe_2.5O₄@Au systems. The resulting GMNPs enable a 10-fold sensitivity enhancement over conventional AuNPs-based lateral flow immunoassays following magnetic enrichment. These findings establish surface ligand coverage as a molecular parameter for programming heterogeneous growth at ferrite-gold interfaces.