This study investigated the effect of different cooking methods (sous vide—SV, steaming—ST, boiling—BT, microwaving—MW, roasting—RT, and sous vide combined with microwaving—SM) on the flavor characteristics of duck meat by gas chromatography—ion mobility spectrometry (GC-IMS), gas chromatography--mass spectrometry (GC-MS) with odor activity values (OAVs) and sensory evaluation. The GC-IMS identified forty-eight flavor compounds, including their monomers, dimers, and trimer. The contents of esters and furan in SV samples were higher than in other samples, while the contents of aldehydes and hydrocarbon in ST were relatively higher. Seventy-two flavor components and fourteen odor-active compounds were detected by GC-MS combined with OAVs. The concentration of total volatiles was the highest in ST samples, and this was followed by SV and MW. Among them, the characteristic aroma compounds including hexanal, octanal, (E)-2-octenal, nonanal, (E)-2-nonenal, cis-4-decenal, decanal, 2,4-decadienal, (E,E)-2,4-decadienal, 1-octen-3-ol, and 1-octen-3-one were the key contributors to duck meat in different cooking methods. A principal component analysis (PCA) of GC-IMS and GC-MS with OAVs data indicated that there were significant flavor distinctions among duck meat processed in different cooking methods. Sensory evaluation revealed that the scores of overall acceptability were relatively higher in BT, SV, and MW samples than other samples, and the umami value was the highest in MW. Thus, ST, SV, and MW could be used to better maintain the flavor quality of duck meat, and the results provided guidance for duck meat producers.