The characteristics of the flow field in completly mixed biogas digester were studied by computational fluid dynamics (CFD). Effects of different installation way of agitator to the disturbances in the upper and lower layer were analyzed. The results showed that increasing of agitator mounting height was difficult to improve the flow. Therefore, the double-mixing was used in the biogas digesters. Compared to the original installation, flow speed could increase by 90.90% in the 4.3m layer and 20.94% in the 0.2m layer with the double-mixing. The actual project also showed that this modified method could reduce scum, disturb sludge and improve operational efficiency.