A cover glass and a manufacturing method thereof are provided, the method includes: coating a first organic layer on a transparent substrate; forming first via holes on the first organic layer at intervals, heating and melting the first organic layer to flow; wet-etching the transparent substrate having the first organic layer to form a first microstructure on a region of the transparent substrate not shielded by the first organic layer; and removing the first organic layer form the transparent substrate. The present disclosure breaks the limitation for preparing microstructures with size below 5 μm in the existing photolithography process, the organic material in wet-etching process can be controlled by heating to make the organic material melted to flow. The size of the microstructure can be reduced and flexibly adjusted according to the pixel size of display panel, the speckle effect of the display device caused by anti-glare treatment can be reduced.