Bio-enzyme was used to stabilize the marine soils of Ningbo. Strength tests, XRD tests and SEM tests were used to analyze the strength and microstructure properties of bio-enzyme and cement stabilized soil. The results of strength tests show that the bio-enzyme not only has obvious reinforcing effect when added alone, but also can promote the solidification of cement. The results of XRD tests show that there is no new substance formation during the solidification process when only bio-enzyme added, which indicates that the process is a physical effect. The results of SEM tests show that the bio-enzyme can improve the pore arrangement, pore morphology and pore size of the soil, and reduce the directional fractal dimension, probability entropy, porosity fractal dimension and pore shape fractal dimension, which makes the orientation of the pores better, the order of the particles higher, the pore size more uniform, and the degree of particle agglomeration higher, therefore increasing the strength. In all the microstructure parameters, the fractal dimension of pore morphology has the greatest influence on the strength of stabilized soil, that is, promoting the aggregation of soil particles is the main role of bio-enzyme in improving the strength of stabilized soil.