The direct determination of glycopeptides and phosphopeptides in type 2 diabetes (T2D) samples is challenging due to their low abundance and the complexity of the sample matrix. To address this, we present a novel strategy by weaving organic linkers into a hydrogen-bonded organic framework (HOF), which is subsequently transformed into a metal-organic framework (MOF) via lanthanide ions (Ln³⁺). The resulting porous composite exhibits bifunctional properties, combining hydrophilic interaction liquid chromatography (HILIC) and immobilized metal ion affinity chromatography (IMAC), which enables the highly efficient simultaneous enrichment of glycopeptides and phosphopeptides directly from serum without extra pretreatment. The enrichment mechanism and possible binding modes were investigated by theoretical calculations. Based on this approach, 142 glycopeptides and 27 phosphopeptides were identified in serum from early-stage T2D patients and controls, respectively. This work successfully overcomes the hurdle of detecting low-abundance post-translational modification (PTMs) in complex clinical samples and opens new avenues for biomarker discovery in T2D through liquid biopsy.