The invention discloses a microalgae harvesting method and application thereof, belonging to the field of microalgae biology. The method comprises the following steps: culturing microalgae and supplementing a trivalent iron ion compound used as a nutritional component for microalgae culture into a culture solution when the culture solution has an OD680 value of 1 to 10 and a pH value of 7.5 to 14; and separating microalgae after layering and settlement of microalgae in the culture solution. The method does not influence the properties of the culture solution, enables the culture solution (including algal species in the culture solution) can be repeatedly used, is free of discharge of waste liquid and beneficial for gathering and harvesting of microalgae, allows collection of microalgae to be simple and reduces cost for collection of microalgae.