Architectural design is essential to achieve ideal chemical and biological properties of nanomaterials. In this article, a novel route to fabricate high-quality magnetic composite microspheres composed of a high-magnetic-response magnetic colloid nanocrystal cluster (MCNC) core, a poly(methylacrylic acid) (PMAA) interim layer, and a Ti4+-immobilized poly(ethylene glycol methacrylate phosphate) (PEGMP) shell via two-step distillation–precipitation polymerization is presented. The unique as-synthesized MCNC@PMAA@PEGMP-Ti4+ composite microsphere is investigated for its applicability for selective enrichment of phosphopeptides from complex biological samples. The experiment results demonstrate that, by taking advantage of the pure phosphate–Ti4+ interface and high Ti4+ loading amount, the MCNC@PMAA@PEGMP-Ti4+ composite microsphere possesses remarkable selectivity for phosphopeptides even at a very low molar ratio of phosphopeptides/nonphosphopeptides (1:500). The extreme sensitivity, excellent recovery of phosphopeptides, and high magnetic susceptibility are also proven. These outstanding features demonstrate that the MCNC@PMAA@PEGMP-Ti4+ composite microspheres have great benefit for the pretreatment before mass spectrometric analysis of phosphopeptides. Furthermore, the performance of the approach in selective enrichment of phosphopeptides from drinking milk and human serum gives powerful evidence for its high selectivity and effectiveness in identifying the low-abundant phosphopeptides from complicated biological samples.