Provided are an array substrate and a manufacturing method thereof, the manufacturing method includes: forming a first active layer on a base substrate; forming a second active layer; forming a second gate on the second active layer; forming a first insulating layer covering the first active layer on the second gate; patterning the first insulating layer to form first via holes at both sides of the second gate to expose the second active layer; depositing a first metal layer in the first via holes and on the first insulating layer; patterning the first metal layer, removing a part of the first metal layer above the first active layer to expose the first insulating layer; etching the first insulating layer using the patterned first metal layer as a mask, forming second via holes above the first active layer to expose the first active layer; cleaning the exposed first active layer.