Abstract: Flaxseed-based milk has great potential for health promotion and disease prevention, due to its rich in α-linolenic acid and plant-derived nutrients. However, the tough seed coat of flaxseed is covered with dense protective layers, such as colloids and fibrous cells, which severely limits the effective release of endogenous proteins, fats and nutrients in flaxseed-based milk. Moreover, the presence of cyanogenic glycosides in flaxseed also increases the obstacles to the daily consumption of flaxseed-based milk. Therefore, it is necessary to enhance the dissolution of nutrients with the reduced antinutritional factors for the high quality and safety of the flaxseed milk. Furthermore, food safety, nutrition, sensory properties and stability can also be strengthened for the development of the flaxseed-based milk industry. In this study, moisture modulation and microwave processing were combined to prepare the flaxseed-based milk. A systematic evaluation was made to clarify the effects of moisture and microwave treatment on the physical and chemical stability, nutrient dissolution, safety index-cyanogenic glycosides content, and volatile components of flaxseed-based milk. The highly toxic hydrocyanic acid was evaporated along with the moisture during the microwave process, and then rapidly reduced the cyanogenic glycoside content of the seeds. Moderate moisture modulation (<17%) reduced the microwave energy absorption of flaxseed, in order to avoid the destruction of the oil body membrane structure for the high stability of the system. In addition, the contents of total phenolics and lignans in flaxseed-based milk with the moisture (20%) treatment were 1.77 and 1.66 times higher than those without moisture treatment. Notably, the total phenols and lignans in the flaxseed-based milk increased sharply, when the moisture content increased to 12.79%, but slowly increased as the moisture content continued to increase, especially the lignans. Microwave treatment promoted the molecular vibrations in the flaxseed constituents, and then destroyed the integrity of the cell wall, as well as breaking the glycosidic bonds via high-frequency electromagnetic waves. During microwave irradiation, the moisture molecules were penetrated mainly from the inside out, leading to drastic changes in the cell structure for the migration and dissolution of nutrients. Therefore, proteins and polysaccharides in natural complex systems were more conducive to the dissociation from compounds. But the moisture modulation was adverse to the production of flaxseed-based milk flavor. Meanwhile, the excessive input of microwave energy caused the extreme distortion of molecules, even the breaking of valence bonds, leading to the irreversible degradation of nutrients. The flavor properties of the flaxseed-based milk were enhanced to increase the microwave terminal temperature. There was a 105-fold increase in the nutty flavor and an 81-fold increase in roasted nut, coffee and sweet flavor in the flaxseed-based milk after 8 min of microwave. Furthermore, the flavor value of flaxseed-based milk was reduced after further excessive microwave (microwave time 10 min), due to the decomposition of aroma substances. Thus, the appropriate moisture content and microwave input can be expected to ensure the edible safety and nutritional quality of flaxseed-based milk. The combined treatment of moisture modulation (12.79%) and microwave (8 min, 140-145 ℃) promoted the dissolution of nutrients for the higher flavor value, thus improving the comprehensive quality of flaxseed milk. The findings can provide theoretical and data support for the high-value production of flaxseed plant-based milk.