Soil disturbance has always been the major concern in shield tunneling activity. This paper presents the investigation on the micro-scale responses of the soils during shield tunnel excavation in sandy-cobble stratum. The code paraEllip3d is employed in discrete element method (DEM) analysis in which the soils are mimicked as an assembly of ellipsoids. Triaxial tests on the micro-scale responses of cobbles are carried out using the materials sampled from the tunnel face during construction period, and corresponding DEM simulations are performed to calibrate the micro parameters for the ellipsoids. On this basis, the face instability process during the shield tunneling in cobbles is studied using 1 g model test as well as corresponding DEM simulation. The micro-scale responses of cobbles are investigated by triaxial test as well as corresponding DEM simulations. Multiple material responses are discussed in the DEM simulations, including the stress-strain relationship, the contact distribution, and the force chain evolution in the elementary and model test. Finally, the mechanism of tunnel face instability in cobbles are discussed on the basis of aforementioned investigations.