Abstract: Flaxseed milk has been one of the most emerging plant-based dairy alternatives, due to its nutritional benefits and unique flavor profile. However, the key aroma compounds can be highly influenced by processing approaches. It is essential to clarify the different preparation steps on its sensory characteristics. This study aimed to systematically investigate the effects of various preparation stages (including microwave treatment, soaking, and homogenization) on the aroma compounds and endogenous enzyme activities in flaxseed milk. Processing techniques were then optimized to enhance the overall flavor quality of flaxseed milk for consumer acceptability. Solid-phase microextraction was employed to combine with the gas chromatography-mass spectrometry (SPME-GC-MS). Nine compounds of the key aromas were identified and quantified in the flaxseed milk. Among them, the (E,E)-2,6-nonadienal and 1-octen-3-ol greatly contributed to the characteristic aroma. Additionally, the activities of five endogenous were measured, such as the enzymes-lipoxygenase (LOX), peroxidase (POD), lipase (LPS), hydroperoxide lyase (HPL), and phospholipase A2 (PLA2). A systematic analysis was also made on their correlation with the formation of aroma compounds. Enzymatic reactions were dominated in the lipid oxidation and volatile compound generation. The key factors were then taken from the sensory attributes of flaxseed milk. The results demonstrated that the activities of all five endogenous enzymes decreased significantly during processing, which directly impacted the generation of volatile aroma compounds. A strong negative correlation was observed between the enzyme activity and the production of aldehydes, pyrazines, alcohols, and phenols. The enzymatic degradation was dominated to modulate the flavor profile of flaxseed milk. Microwave treatment was found to particularly enhance the aroma release. The total content of the nine key aroma compounds significantly increased from 215.90 μg/kg to 587.32 μg/kg during processing. The reason was primarily attributed to the heat-induced acceleration of Maillard reactions and lipid oxidation. These pathways of reaction were facilitated to form the volatile compounds, especially the pyrazine-derived aroma compounds. Pyrazines were also characterized by roasted, nutty, and caramel-like notes. There was a positive contribution to the overall flavor perception of flaxseed milk. Furthermore, microwave treatment reduced the release of undesirable aldehydes during lipid oxidation. Thereby, the off-flavors were minimized to improve the sensory acceptability of the final products. The soaking was also used to modify the flavor profile of flaxseed milk. The overall sensory experience was improved to effectively reduce the content of undesirable volatile compounds, including the aldehydes and ketones that are associated with the rancid and grassy notes. The (E, E)-2, 4-Heptadienal was also reduced, due likely to the enzymatic deactivation and the leaching of certain precursors into the soaking medium. Their transformation into volatile compounds was prevented from negatively impacting the aroma quality. Homogenization further contributed to the flavor enhancement. The release and dispersion of aroma compounds were facilitated over the flaxseed milk matrix. The stability and consistency of the products were improved for the more uniform distribution of volatile compounds, indicating the enhanced attributes of sensory. The mechanical forces during homogenization also disrupted the cellular structures, allowing for the better extraction and retention of desirable aroma compounds. Therefore, there were complex interactions between different preparations and the aroma profile of flaxseed milk. An effective strategy of aroma enhancement was coupled with microwave treatment with controlled soaking and homogenization. The sensory quality of flaxseed milk was also optimized after treatment. The desirable compounds of pyrazine-based aroma were formed to reduce the off-flavors after the lipid oxidation. Microwave treatment also served as a valuable tool to improve the flavor characteristics. Meanwhile, the soaking effectively mitigated the off-flavors. The homogenization also further enhanced the sensory perception under the uniform distribution of volatile compounds. A theoretical foundation was provided for the refining processing in the plant-based dairy industry. Additional parameters were further considered to enhance the aroma and overall quality of flaxseed milk, such as the temperature, enzyme inhibitors, and alternative processing. Additionally, the sensory evaluation and consumer preference analysis were also essential to validate the practical applicability in the commercial production of flaxseed milk. Ultimately, the flavor profile of flaxseed milk was optimized to serve as a sustainable and appealing alternative to conventional dairy products.