The invention relates to a low-water-absorption good-appearance flame-retarding polyamide composition and a preparation method thereof. The polyamide composition is prepared from, by weight, 45-65 parts of MXD6 and 35-55 parts of PA66 (the sum of weight parts of the MXD6 and PA66 is 100 parts), 15-45 parts of polyamide functional master batch, 20-70 parts of glass fibers, 5-15 parts of a flame retardant, 2-10 parts of a synergist, and 0.5-3 parts of a processing aid; wherein the polyamide functional master batch is composed of, by weight, 25-55 parts of PA66, 30-60 parts of polyketone, 10-30 parts of organic silicon, 2-6 parts of a nano-oxide, 1-5 parts of polyethylene glycol, 0.06-0.3 parts of toluene diisocynate, and 0.01-0.06 parts of dicumyl peroxide. The polyamide composition has excellent flame-retarding effect and mechanical performance, is low in water absorption, is free of floating fibers on the surface, is low in warping and is anti-scraping.