Yak meat is in high demand due to its unique flavor. Thus this research utilized GC × GC-ToF-MS to discover important flavor compounds in yak meat raised during the cold season under different feeding systems: traditional grazing (TG), grazing-based supplementation (GS), and stall-feeding (SF). Meat quality results showed that SF significantly improved meat's lightness and tenderness (P <
0.05), as compared to TG. Intramuscular fat (2.7 g/100 g) was highest in the SF, followed by the GS (2.46 g/100 g) and the TG (1.57 g/100 g), whereas protein content was similar in the GS and TG, but again higher in the SF. β-carotene and Vitamin E were highest in the GS and TG groups (P <
0.05), respectively. Essential, fresh, and total amino acids were richer in the SF and TG than in the GS group (P <
0.05). TG exhibited a significantly elevated level of n-3 PUFA compared to the SF and GS systems (P <
0.05). Flavoromics analysis identified 736, 721, and 869 flavor substances in the TG, GS, and SF groups, respectively with six as key flavor compounds (ROAV ≥ 1) in all belonging to aldehydes, ketones, and heterocyclic compounds. The pyruvate, glycolysis/gluconeogenesis, and phenylalanine metabolic pathways significantly contributed to the yak meat flavor. Network analysis showed a complex significant positive correlation between amino acids in meat and Vitamin A in fodder (P <
0.05). Altogether, this study provides a basis for selecting a suitable meat production system that benefits producers and consumers by ensuring an annual supply of fresh meat.