To investigate physicochemical properties of soymilk made from soybean varieties with special protein composition，the effect of homogenization (80MPa) and heating (95℃for 25min) on physicochemical characteristics of soymilk prepared respectively from soybean genotype lacking lipoxygenase (Dongfu 3) and soybean lacking 7S globulin (Dongfu 2) was studied with ordinary soybean variety of Heinong 64 as control. The result showed that raw soymilk made from Dongfu 3 soybean null in lipoxygenase showed higher protein solubility, free sulfydryl group content and lower average particle size, turbidity, apparent viscosity, centrifugal precipitation percent than the other varieties evaluated before homogenization and heating, but raw soymilk prepared from Dongfu 2 soybean lacking 7S showed the lowest protein solubility, free sulfydryl group content and highest average particle size, turbidity, apparent viscosity, centrifugal precipitation percent, which meant the physical stability of Dongfu 3 raw soymilk was the highest and Dongfu 2 raw soymilk was the lowest among the all varieties evaluated before homogenization and heating. After homogenization, the protein solubility, free sulfhydryl content of all soymilk was increased, and the average particle size, turbidity and viscosity were decreased. Centrifugal precipitation percent of Dofu 2 and Heinong 64 soymilk was reduced significantly after homogenization （p<0.05).Though there was no significant difference in the centrifugal sedimentation percent between the homogenized and unhomogenized Dongfu 3 soymilk （p>0.05), the physical stability of DongFu 3 soymilk was still the highest and Dongfu 2 soymilk was the lowest after homogenization. After heating, the protein solubility, average particle size, turbidity and apparent viscosity of three varieties of soymilk were increased, while the free sulfhydryl group content and centrifugal precipitation percent were decreased. Although both heating and homogenization had a marked effect on the increase in the protein solubility and decrease in the centrifugal precipitation percent of soymilk, heating more significantly improved the protein solubility and physical stability of soymilk compared with homogenization （p<0.05). The average particle size and centrifugal precipitation percent of Dongfu 3 soymilk were still the lowest after heating. Although the average particle size of Dongfu 2 soymilk was increased more significantly than that of Dongfu 3 and Heinong 64 after heating, higher apparent viscosity contributed to the great reduction of the centrifugal precipitation percent so that the physical stability of heated Dongfu 2 soymilk was more superior than that of heated Heinong 64. Confocal fluorescence micrographs showed the oil droplet size distributions of three varieties soymilk were consistent with the result of particle size before and after homogenization and heating.