Human health is always under global spotlight, but now it suffers from severe environmental issue and various diseases.Developing highly selective and effective extraction technique for environmental pollutant removal and target protein/peptide molecules conduces to the solution of environmental contamination and early disease detection, which will promise human health to a great degree. Metal-organic frameworks（MOFs） are typical porous nanomaterials featuring rigid structure, large specific surface area, thermal and chemical stability, numerous active sites and easy functionalization. Moreover, multitudinous combination of metal centers and organic ligands often endows MOFs with structure and function diversity. Owing to such splendid merits, MOFs are able to act as advanced adsorbents for sample-pretreatment in proteomics and environmental field,which indicates great efficiency, reproducibility, convenience and cost-effectiveness. In this review, the novel design of MOFs and their applications in proteomics and environmental research are roughly summarized. We first introduce the representative researches of functional MOFs in protein post-translational modifications including glycosylation and phosphorylation, mainly focusing on hydrophilic interaction liquid chromatography（HILIC） or metal-oxide affinity chromatography（MOAC）. The important role of MOFs in enzyme immobilization is also covered. Then MOF-based adsorptive removal of diverse environmental contaminants embracing plasticizers, pesticides and varied water pollutants（pharmaceutical and personal care products,organic dyes and heavy metals）, in which multiple chemical and non-chemical interactions play a vital role, is emphatically discussed. Finally, we analyze the existing problems and challenges in the way of wider practical applications and put forward prospective anticipation.