Application of soya proteins (SP) in flaxseed oil microencapsulation based on complex coacervation was investigated. The effects of SP/gum arabic (GA) mixing ratio (1:2, 1:1 and 2:1) and pH (2.80, 3.15 and 3.75) on coacervate preparation were studied firstly. The highest coacervate yields (CY) were achieved at SP/GA = 1:1, pH 3.15, and SP/GA = 2:1, pH 3.75, which were 81.2 ± 2.0%, 88.1 ± 0.6%, respectively. Thereafter, the microencapsulation of flaxseed oil was detected in accordance with the results of the coacervation of SP/GA, that is the optimal condition for microencapsulation was corresponded to the condition where CY was the highest. Under the conditions of SP/GA = 1:1, pH 3.15, and SP/GA = 2:1, pH 3.75, the microencapsulation efficiency and total yield reached 81.5 ± 0.1% and 81.7 ± 0.4%, and 77.4 ± 3.7% and 86.7 ± 2.4%, respectively. Microscopic morphology revealed that the formation of a biopolymer shell around the oil droplets was achieved at specific conditions.