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On-demand customization of materials with tailored structures and properties is a long-standing goal in materials science. Yet conventional materials often exhibit complex configurations, hindering unified design principles and limiting performance optimization. Here, utilizing modular graphdiyne (GDY) as a configurable platform, we present a chemically guided molecular design framework to achieve atomic-level precision control over catalytic behaviors. By combining density functional theory (DFT) with experimental validation, we systematically introduced electron-donating and electron-withdrawing groups to construct 13 organic molecular units, yielding modularly customizable GDYs with predetermined structures, enabling us to disentangle the interplay between structure and catalytic function. We identified a volcano-shaped correlation, linking the oxidation state of the active alkyne carbons to CO2 reduction (CO2RR) activity. Furthermore, we established that this oxidation state is directly correlated with intrinsic electronic descriptors, including work function, VBM, and Fermi level (Ef)─constructing a predictive framework. In particular, by precisely tuning the oxidation state of sp-hybridized carbons, we showed that GDYs can rationally optimize intermediate binding energies and effectively resolve the conventional trade-off between the CO2RR activity and HER suppression. This mechanistic approach enables systematic control of the CO/H2 ratio from 1:10 to 13:1. Notably, the fluorinated GDY (3FGDY) achieves a remarkable 93% CO Faradaic efficiency with sustained stability over 90 h. These findings establish a direct atomic-level structure–performance relationship and provide a robust proof-of-concept for modular materials design, with promising implications for syngas production and sustainable energy conversion.