Abstract: Cement and lime materials are always used to reinforce muddy soft soil in the project, but the long-term strength of the reinforcing soil is affected by the organic matter of humic acid in the soil which will hinder the formation of cement gelling substances. Using bio-enzyme reinforcement can effectively reduce the impact of organic matter, but the aging characteristics of reinforcement are not clear. In order to explore the change of physical property index of reinforced muddy soft soil with time. Two typical biological enzymes (Terra, E3) were selected as research object to carry out undrained unconsolidated triaxial shear test and microscopic structure test combined with optical microscopy and electron microscopy for reinforced soil samples, the results show that after adding two type of Bio-enzyme (TerraZyme and E3), the mucky soft soils’ shear strength improved 316.2% and 287.3% at least compared to undisturbed soil. The TarraZyme’ improved soil forms a compact plate structure at the micro level. And it increases the shear strength of soil by raising internal friction angle. The Irregular spherical structure or agglomerate structure was formed by the Bio-enzyme of E3.It strengthens the bonding between particles and increases the cohesion to accomplish the purpose of strengthening soil. And the Bio-enzyme had played a non-monotony increased role in the time domain. From the 7th day, the strength of the bio-enzyme-reinforced soil sample has an advantage over the blank control group. By 60 days, the intensity gradually approached the blank control group. There are obvious reinforcement stages(7~60 days)and decline periods (60~90 days) in its effect. The research results have good application value and theoretical significance for the engineering problem solving of biological enzyme-reinforced silty soft soil.