The stability of coastal soft soil stratum is dramatically affected by external construction. To clarify the disturbance mechanism of the shallow shield tunnel engineering to the stratum, a refined numerical model for simulation of shield dynamic excavation was established based on the finite difference scheme, and the disturbance effect of every construction factor on the stratum was studied according to the modeling results. In the model, the combined effects of four factors on surrounding soil, including cutter head friction, excavation supporting force, grouting pressure, and shield friction, were considered. Referring to the behavior change of the grouting layer in the practical project, the relationship between pressure dissipation and slurry solidification during the shield tail grouting was divided into three stages to simulate the flowing state, the initial setting state and the final setting state of the slurry, respectively, and the corresponding parameters were sectionally assigned to the grouting layer of the newly-built tunnel and adjusted in real-time along with the excavation process. This model can realistically reflect the whole process of shield tunneling and realize the refined simulation of the construction. The numerical model was verified by comparison with the results from the field monitoring of the shield tunnel project with 1.0D (D is the outer diameter of the tunnel) burial depth in Xiamen Metro, and the influence of the above four construction factors on the soft soil stratum disturbance during the shallow excavation process was calculated and compared, and the effect of the factors on the disturbance deformation was summarized. The results show that the cutter head pushing causes the radial expansion of the forward soil. In the grouting process, a settlement groove is formed within 1.0D on both sides of the excavation space, and the near-field rebound and far-field expansion occur to the soil lateral displacements on two sides of the tunnel during the solidification of the grouting layer. The increase of the cutter head friction and shield friction will further aggravate the stratum disturbance deformation, and with the increase of the excavation supporting force and grouting pressure, the surface settlement slightly slows down and the stratum lateral displacement significantly increases. The results are of guiding significance for disturbance prediction and parameter selection in shallow shield excavation