An array substrate and a manufacturing method thereof as well as a display panel are provided. The manufacturing method comprises: forming a pattern including a scanning line (32) and a spacer base (33) on a same layer of a substrate (31); forming a gate insulating layer (34); forming a pattern including an active layer (35), a data line, a source electrode and a drain electrode; forming a passivation layer (36); sequentially etching the passivation layer (36) and the gate insulating layer (34) through a dry etching method to form a via hole (38) exposing the spacer base (33), and inducing materials generated from an etching process in a reaction cavity to deposit on a surface of the spacer base (33) through an electric field formed by the spacer base (33) exposed in the via hole (38) and etching gas adopted in the etching process, to form a spacer (39).