The invention discloses a protein, a gene and a function fragment involved in palmitic acid synthesis and application thereof. The invention provides a protein composed of amino acid sequences shown by a sequence 6, a sequence 4 or a sequence 2 in a sequence table, a DNA (Deoxyribonucleic Acid) molecule shown by a sequence 5, a sequence 3 or a sequence 1 in the sequence table, and a DNA fragment shown by a sequence 7. In the invention, a recombinant inbred strain colony is constructed by utilizing a common material B73 and a high oil system By 804, a major QTL-Pa 19 for controlling corn oil palmitic acid is positioned on a ninth chromosome 9.02 Bin, and the LOD (Level of Detail) of the major QTL-Pa can reach 27, and can be used for interpreting 42% of genetic variation. By means of the method of based cloning, the invention accurately positions the major QTL-Pa for controlling the palmitic acid content of corn kernels and the proportion of kernel saturated/unsaturated fatty acid in Beijing high oil, clones the function gene of QTL-Pa 19, probes the functional sites thereof, develops the functional markers, and has great value for improving the quality of corn kernels.