A method for mutagenizing and selectively culturing a refractory single-cell green alga includes such steps as sterilizing and cooling culture medium, inoculating alga liquid, culturing, mixing with iodine solution or bromophenol blue, deactivating, calculating alga density in alga liquid, ultraviolet mutagenizing, dark culturing, mixing the cultured alga liquid with fresh culture medium, culturing, high-temp screening, amplifying culture of living alga cells, culturing under light radiation, inoculating yellow alga, culturing, testing its mutagenized effect, measuring the long and short diameters of cell, extracting DNA, random amplifying of polymorphic DNA, calculating genetic similarity coefficient, extracting H-42 and general protein, electrophoresis, dyeing with Coomassic brilliant blue, recording result and observing the electropherogram to obtain result.