When it comes to the early detection of colorectal cancer (CRC), the study of protein phosphorylation is crucial. This work used magnetic covalent organic framework (COF) materials as substrates. The magCOF@PM-Ti4+ composites were obtained by constructing the three-dimensional cross-linked structures and chelating them with Ti4+ in a green and economical way, which was utilized to identify the phosphopeptides. This material possesses magnetic properties that facilitate simplified experimental manipulation, has superior sensitivity (0.2 fmol), excellent selectivity (1000:1), and good reusability (10 cycles), and achieves outstanding recovery rates (103.4 ± 1.2%). In addition, magCOF@PM-Ti4+ was utilized to identify phosphopeptides in human serum. One hundred phosphopeptides were identified from three normal control serums, whereas 98 phosphopeptides were identified from three CRC serums. The results demonstrated that magCOF@PM-Ti4+ has great potential in efficiently identifying low-abundance phosphopeptides.