The invention relates to the field of nitride semiconductor vertical-cavity surface-emitting lasers, and discloses an active region structural design method of a multi-wavelength GaN-based vertical-cavity surface-emitting laser. The active region structural design method comprises the step of designing laser cavity length, quantum dot positions and quantum dot sizes. Through the precise design ofthe sizes of multi-layer quantum dots and spatial positions thereof in a resonant cavity, the maximum coupling between light emitting of the quantum dots of different sizes and corresponding cavity modes and a standing wave optical field in the cavity is realized, thus a plurality of laser modes can obtain large enough gain simultaneously and stable multi-wavelength laser output is realized finally. Meanwhile, the invention further provides a specific device structure of the multi-wavelength GaN-based vertical-cavity surface-emitting laser manufactured by adopting the active region, and application thereof.