Simple SummaryThe type and quantity of fat are among the key factors influencing the carcass and meat quality in yak. The effect of gender to fat in yak and the correlation of meat quality with fat were studied in this paper. The meat of male yaks (MYs) is healthier from the point of nutritional value, whereas the meat of female yaks (FYs) possesses better qualities in relation to the visual impact and mouthfeel. The below results can provide a theoretical basis for the deep processing of yak meat. Yak meat quality (especially tenderness) can be improved by increasing the content of fat, C18:0, cis-C18:2, and cis-C18:1 in muscle during yak production. These genes, including SCD, PLIN5, LPL, ME1 and DBI, play a crucial role in the regulation of fat deposition in yak. Above candidate genes for fat deposition in yak can supply the theoretical basis in molecular breeding of yak with a high fat content in muscle.This study aimed to explore the differences in fat deposition between female (FYs) and male yaks (MYs). Compared with MYs, the tenderness, L*, marbling, absolute content of fat, and most fatty acids (FAs) of longissimus dorsi (LD) in FYs were higher or better (p < 0.05), whereas the relative content of polyunsaturated fatty acids (PUFAs) and n-3 PUFAs were lower (p < 0.01). The absolute content of fat, C18:0, cis-C18:2, cis-C18:1, and C24:0 were positively correlated with L*45 min, b*24 h, tenderness, and marbling score of LD in FYs and MYs (p < 0.05), respectively. LPL, FATP2, ELOVL6, HADH, HACD, and PLINS genes play a crucial role in improving the marbling score and tenderness of yak meat. The results of gene expression and protein synthesis showed the effect of gender to FA biosynthesis, FA transport, lipolysis, and FA oxidation in the adipose tissue of yak was realized by the expressions of ME1, SCD, ACSL5, LPL, FABP1, PLIN4, and PLIN2 in peroxisome proliferators-activated receptor (PPAR) signaling. This study established a theoretical basis for the improvement of the meat quality of yak and molecular breeding.