Isomerism in covalent organic frameworks (COFs) has scarcely been known. Here, for the first time we show 3D COFs with three framework isomers or polymorphs constructed from the same building blocks. All isomers were obtained as large (>10 μm) crystals; although their crystal shapes were distinctly different, they showed identical FT-IR and solid-state NMR spectra. Our structural analyses revealed unprecedented triple isomerism in 3D COFs (noninterpenetrated dia, qtz, and 3-fold interpenetrated dia-c3 nets). Furthermore, this Communication reports the first known COF with qtz topology for which the structure determination was based on Rietveld analysis. We achieved triple framework isomerism by reticulating a tetrahedral building block with a flexible junction and a linear building block with PEO side chains and by varying solution compositions. Our energy calculations, along with the discovery of interisomer transition, revealed that the isomer with qtz topology was a kinetic isomer. Thus, this simple yet little-explored concept of reticulating only flexible building blocks is an effective pathway to significantly broaden the diversity of 3D COFs, which have been proposed for a myriad of applications.