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Abstract Tuning the topology of two‐dimensional (2D) covalent organic frameworks (COFs) is of paramount scientific interest but remains largely unexplored. Herein, we present a site‐selective synthetic strategy that enables the tuning of 2D COF topology by simply adjusting the molar ratio of an amine‐functionalized dihydrazide monomer (NH₂−Ah) and 4,4′,4′′‐(1,3,5‐triazine‐2,4,6‐triyl)tribenzaldehyde (Tz). This approach resulted in the formation of two distinct COFs: a clover‐like 2D COF with free amine groups (NH₂−Ah−Tz) and a honeycomb‐like COF without amine groups (Ah−Tz). Both COFs exhibited good crystallinity and moderate porosity. Remarkably, the clover‐shaped NH₂−Ah−Tz COF, with abundant free amine groups, displayed significantly enhanced adsorption capacities toward crystal violet (CV, 261 mg/g) and congo red (CR, 1560 mg/g) compared to the non‐functionalized honeycomb‐like Ah−Tz COF (123 mg/g for CV and 1340 mg/g for CR), underscoring the pivotal role of free amine functional groups in enhancing adsorption capacities for organic dyes. This work highlights that the site‐selective synthetic strategy paves a new avenue for manipulating 2D COF topology by adjusting the monomer feeding ratio, thereby modulating their adsorption performances toward organic dyes.