In order to deal with wastewater with high soy protein effectively, a technology of two-stage foam fractionation, which could increase both enrichment ratio and recovery of soy protein, was developed based on the research of the influences of initial pH value, superficial air flow rate and temperature, specially at higher temperature (60℃) on foam fractionation. When soy protein concentration of the wastewater was 4.0 g/L, enrichment ratio at 60℃ was four times higher than that at the normal temperature. When the conditions of the first stage of the two-stage foam fractionation were soy protein concentration of the wastewater as 4.0 g/L, initial pH value of the wastewater as 7.0, superficial air flow rate as 0.133 cm/s and temperature as 60℃, enrichment ratio of soy protein was 7.71, and the residual solution was fed to the second stage as the feed stream. The second stage run at 20℃ and 0.133 cm/s for superficial air flow rate, firstly, when no foam stream overflowed from the top of foam fractionation tower, superficial air flow rate was increased to 0.398 cm/s, and enrichment ratio of soy protein reached 2.63, and then the foamate was added to the wastewater as the feed stream of the first stage. The total recovery of the two-stage foam fractionation was 82.75%. Two-stage foam fractionation at different temperatures and superficial air flow rates can be used efficiently for the wastewater treatment and soy protein recovery.