The spinel-type magnetic manganese ferrite (MnFe2O4) microspheres synthesized by simple solvothermal method were used as a novel adsorbent for selective enrichment and effective isolation of phosphopeptides. The uniform MnFe2O4 magnetic affinity microspheres (MAMSs) had a narrow particle size distribution between 250 and 260 nm, and displayed superparamagnetism with a saturation magnetization value of 67.0 emu/g. Comprehensively, the possible formation mechanism of MnFe2O4 microspheres with ferric and manganous sources as dual precursors was elucidated by comparison with those of Fe3O4 nanoparticles and MnOOH nanosheets respectively with either ferric or manganous source as single precursor. It was suggested that the spherical or sheet nanostructures could be achieved via secondary recrystallization or Ostwald ripening. The MnFe2O4 MAMSs probe exhibited excellent dispersibility in aqueous solution, and rapid magnetic separation within 15 s, as well as good reusability. More importantly, MnFe2O4 was highly selective for phosphopeptides because of the strong coordination interaction between metal ions (Fe3+ and Mn2+) and phosphate groups of phosphopeptdies. This high specificity was demonstrated by effectively enriching phosphopeptides from digest mixture of beta-casein and bovine serum albumin (BSA) with high content of non-phosphopeptides, and embodied further in phosphopeptides enrichment from non-fat milk digests and human serum. Consequently, the prepared MnFe2O4 affinity materials are expected to possess great potential in phosphoproteome research.