To improve the utilization of mulberry seed with its extremely high annual yield and stress the importance of mulberry seed oil, mulberry seed oil and α-linolenic acid (ALA) were used to prepare structural lipids (SLs) with a balanced ratio of n-6/n-3 polyunsaturated fatty acids (PUFAs) in a microfluidic enzyme reactor. When the lipase amount was 1/3 g/cm³, the substrate molar ratio was 1:5, the flow rate was 2 µL/min and the reaction temperature was 50 °C, the n-6:n-3 ratio of SLs was 1.11:1, and the content of ALA reached 42.0%. The prepared SLs that contained 89.7% PUFAs had a lower melting temperature (-24.2 °C) and a lower crystallization temperature (-40.1 °C) compared with mulberry seed oil, and had three stages of weight loss during processing. These results implied that the SLs were more stable than mulberry seed oil, more beneficial to human health, easier to absorb and convenient to store. [ABSTRACT FROM AUTHOR]