The invention discloses a labeling method of an apple pollen tube microfilament. The labeling method comprises the following steps: cultivating apple pollen, curing the apple pollen, performing enzyme treatment on the apple pollen, treating the apple pollen with a surfactant, performing dye labeling, and performing scanning and imaging. The labeling method has the beneficial effect that the labeling method of gymnosperm pollen tube microfilament is referred and improved on the basis of the labeling method of pear pollen tube microfilament, dyes enter cells easier through curing, enzymolysis of cell walls and the surfactant, the interference of cell outer wall autofluorescence due to insufficient enzymolysis as TRITC-Phalloidin is applied are avoided when FITC-Phalloidin labeling is applied, so that relatively complete apple pollen tube microfilament can be stored; moreover, the labeling method is efficient and quick, can be used for obtaining relatively clear and bright pictures, thus filling up the blank of the apple pollen tube microfilament labeling, providing reference for labeling microfilament in rosaceae and angiosperm pollen tube, and achieving a high application value.