Exploration of valuable information from peptide biomarkers in biological fluids for early diagnosis and elucidation of disease has drawn increasing attention in clinical biomedicine. In this work, a novel affinity probe consisting of magnetic core and mesoporous silica shell incorporated with TiO₂ has been constructed and developed for selective enrichment of endogenous peptides taking advantage of the stronger interaction of TiO₂ to carboxyl groups of the peptides and the size-exclusion effect of the ordered mesopores under mild enriching conditions. Application effectiveness of the porous structured affinity probe with large specific surface area (216.4 m² g⁻¹), narrow pore size distribution (3.0 nm) and high saturation magnetization (49.8 emu g⁻¹) was investigated using standard peptides ([Pyr1]-Apelin-13), digest of bovine serum albumin (BSA) proteins, human urine and serum. The signals of peptides can be amplified more than 100 times after enrichment using the affinity probe, and 44 target peptides with sequence coverage of 59% can be captured and identified from 5 nM BSA digest due to plentiful affinity sites of the affinity probe. Furthermore, the affinity probe can selectively capture peptides from the mixture of peptides and proteins with the molar ratio of 1 : 1000 in virtue of the size-exclusion effect of ordered nanopores. More importantly, the affinity probe is also effective for selective capture of peptides from human urine and serum with high sensitivity. It is expected that this work would be beneficial to rapid capture of potential peptide biomarkers from complex biological samples.