The invention relates to the field of corrosion protection of metal, and aims to provide a method for preparing a compound zinc phosphate series anti-rust pigment by utilizing a rod-pin type nano ballmill. The method comprises the following steps: adding deionized water, an inorganic zinc phosphate series anti-rust pigment, an organic anti-rust pigment and a dispersing auxiliary into a blending barrel to obtain mixed slurry and uniformly performing stirring; starting a cooling circulating water system of the rod-pin type nano ball mill; turning on a diaphragm pump and injecting the mixed slurry into an inner cavity of the rod-pin type nano ball mill and carrying out circular grinding; performing spray drying after grinding so as to obtain the compound organic-inorganic nano zinc phosphateseries anti-rust pigment with the partical size of 100nm or below. According to the method disclosed by the invention, the defects of low dissolvability, poor hydrolysis resistance, low anti-rust activity, effect delay, poor flash rusting resistance ability and the like in the prior art are overcome, the load efficiency of the organic anti-rust pigment on the surface of the inorganic anti-rust pigment can be improved, and the cooperative reinforcement effect between the anti-rust pigments can be fully developed. Through application of the rod-pin type nano ball mill, industrial production ofthe compound organic-inorganic nano anti-rust pigment can be easily realized.