The present invention provides a micro LED array substrate encapsulation structure and an encapsulation method thereof. The micro LED array substrate encapsulation structure of the present invention includes a base plate, a micro LED array, and a photoresist protection layer. The micro LED array includes a plurality of micro LEDs arranged in an array. The photoresist protection layer is formed with a plurality of vias at locations corresponding to the plurality of micro LEDs. The plurality of micro LEDs are respectively located in the plurality of vias. Each of the vias is filled therein with a UV resin microlens that has an upper surface in a bulging form and covers the micro LED in the corresponding one of the vias. The micro LEDs and driving substrates located thereunder can be protected and an effect of light emission of the micro LED array substrate can be improved.