Chiral pyrrolidinyl units are important building blocks in biologically active natural products and drugs, thereupon, searching approaches for the synthesis of diverse structured pyrrolidine derivatives is of great importance. Meanwhile, owing to the special physicochemical properties of fluorine atoms, the introduction of fluorine containing groups into small molecules often change their activities to a great extent. Herein, we reported an efficient route to chiral 3,3-difluoro- and 3,3,4-trifluoropyrrodinyl derivatives by Cu(I)-catalyzed enantioselective 1,3-dipolar cycloaddition of azomethine ylides with less active 1,1-difluoro- and 1,1,2-trifluoroalkenes. A series of new fluorinated pyrrolidines have been prepared in high yields (up to 96%) and excellent stereoselectivities (up to > 20:1 dr and 97% ee), and these unique structural blocks could be readily introduced into some natural compounds and pharmaceuticals. Additionally, antifungal activity investigation against four common plant funguses showed that some products possess general and high biological activities (up to 93% inhibition rate), the comparison with the antifungal activities of corresponding non-fluorinated compounds (low to 13% inhibition rate) revealed that the fluorine atoms at pyrrolidinyl rings play a crucial role in the antifungal activity, which prove the special properties of fluorine atoms in organic molecules.