The invention discloses a baking varnish for a magnesium aluminum alloy base material and preparation and using methods thereof. The preparation method comprises the following steps of: (1) adding polyester modified acrylic resin, epoxy resin, an anti-forming agent, a dispersing agent, a wetting agent, a leveling agent, and a part of solvent in a certain ratio into a stirring kettle sequentially and stirring; (2) adding color paste, filler, and an antisetting agent and stirring in a high speed; and (3) finally adding amino resin, adhesion promoter, and residual solvent and uniformly stirring to finish the whole preparation process of the polyester baking varnish. The using method of the prepared polyester baking varnish for the magnesium aluminum alloy base material comprises the following steps of: weighing the polyester baking varnish for the magnesium aluminum alloy base material, stirring uniformly in the weight ratio of the polyester baking varnish to diluents of 1:(0.4-0.6), spraying to the magnesium aluminum alloy base material, placing for 10 to 20 minutes, baking at the temperature of between 150 and 170 DEG C for 20 to 30 minutes, and baking and curing to obtain the polyester baking varnish layer.