The invention discloses a cotton breeding method treating pollen with cold plasma and application thereof. The cotton breeding method comprises the following steps: 1) plucking parent flowers used for pollination and about to blossom in a cotton breeding material, taking off petals so as to expose pollen in a cold plasma treating machine and carrying out cold plasma treatment; 2) after pollination of pollen having undergone cold plasma treatment, carrying out resistance identification test and variety comparison test so as to obtain an excellent novel cotton hybrid variety and a novel breeding material; 3) subjecting the novel cotton hybrid variety to plantation and separation, selecting single plants to obtain an excellent selfing line and carrying out resistance identification test and variety comparison test so as to obtain an excellent novel conventional cotton variety; and 4) selecting a selfing line of an excellent shape as parents, carrying out hybridization and measurement matching so as to obtain a hybridized cotton combination and carrying out resistance identification test and variety comparison test so as to obtain an excellent novel hybridized cotton variety. With the advanced cold plasma treatment technology, the activity and combining ability of the pollen of cotton can be improved, and the vitality and pollen fertility of distant hybirdization F1 can be enhanced.