The present invention provides a method of manufacturing a thin film transistor and a pixel unit thereof, comprising: forming a metal oxide layer, a gate insulating layer, a gate metal layer and an etching barrier layer on a substrate; through the same mask, etching a part of the etching barrier layer, the gate metal layer and the gate insulating layer on the substrate, while retaining: the metal oxide layer, the gate insulating layer, the gate metal layer and the etching barrier layer in a gate region, and the part of the metal oxide layer, the gate insulating layer and the gate metal layer in source and drain regions for forming contact vias; and exposing the remaining metal oxide layer in the source region and in the drain region; depositing a passivation layer, etching and metallizing the exposed oxide in the source and drain regions to form the source and drain contact vias.