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Enrichment of phosphopeptides is a crucial step in phosphoproteomics study. At present, combination of multiple affinity chromatography is regard as an efficient phosphopeptide enrichment strategy. Therefore, designing and preparing composites with multiple affinity sites is of great significance. Herein, the Oxid-Ti3C2Tx/UIO-66-NH2 composites with multiple affinity sites are rapidly synthesized by dielectric barrier discharge (DBD) technology at low temperature and atmospheric pressure. The in-situ nucleation of UIO-66-NH2 and TiO2 can be flexibly regulated through the feed ratio of MOF precursors and the DBD duration individually. The UIO-66-NH2 has large specific surface area, high porosity and plentiful Zr-O clusters. Oxid-Ti3C2Tx provides abundant exposed Ti sites and Ti-O clusters. Based on these, Oxid-Ti3C2Tx/UIO-66-NH2 composites exhibited high sensitivity (0.1 fmol μL−1), satisfactory selectivity (BSA: α-casein = 100: 1, molar ratio) and superior repeatability for phosphopeptide enrichment. In addition, the composites performed well in biological samples like nonfat milk (24 phosphopeptides), human saliva (15 endogenous phosphopeptides) and human serum (all 4 endogenous phosphopeptides), demonstrating a huge application potential in phosphoproteomics study. More importantly, this study opens a new path to synthesize MXene/MOF composites with controllable oxidation degree and flexible compositions regulation efficiently, revealing its broad application prospects in various fields.