β-Keto-enamine-linked 2D covalent organic frameworks (COFs) have emerged as highly robust materials, showing significant potential for practical applications. However, the exclusive reliance on 1,3,5-triformylphloroglucinol (Tp aldehyde) in the design of such COFs often results in the production of non-porous amorphous polymers when combined with certain amine building blocks. Attempts to adjust the crystallinity and porosity by a modulator approach are inefficient because Tp aldehyde readily forms stable β-keto-enamine-linked monomers/oligomers with various aromatic amines through an irreversible keto-enol tautomerization process. Our research employed a unique protection-deprotection strategy to enhance the crystallinity and porosity of β-keto-enamine-linked squaramide-based 2D COFs. Advanced solid-state NMR studies, including 1D ¹³C CPMAS, ¹H fast MAS, ¹⁵N CPMAS, 2D ¹³C−¹H correlation, ¹H−¹H DQ-SQ, and ¹⁴N−¹H HMQC NMR were used to establish the atomic-level connectivity within the resultant COFs. The Tp_OMe-Sqm COFs synthesized utilizing this strategy have a surface area of 487 m² g⁻¹, significantly higher than similar COFs synthesized using Tp aldehyde. Furthermore, detailed time-dependent PXRD, solid-state ¹³C CPMAS NMR, and theoretical DFT studies shed more light on the crystallization and linkage conversion processes in these 2D COFs. Ultimately, we applied this protection-deprotection method to construct novel keto-enamine-linked highly porous organic polymers with a surface area of 1018 m² g⁻¹.