This article presents an experimental investigation on ductile-mode micro-milling of monocrystalline silicon using polycrystalline diamond (PCD) end mills. Experimental results indicate that the irregular fluctuation of cutting force always induces machined surface failure, even in ductile mode. The internal mechanism has not been investigated so far. The multiscale discrete dislocation plasticity framework was used to predict the dislocation structure and strain evolution under the discontinuous cutting process. The results showed that a mass of dislocations can be generated and affected in silicon crystal. The dislocation density, multiplication rate, and microstructure strongly depend on the milling conditions. In particular, transient impulse load can provide a great potential for material strength by forming dislocations entanglement structure. The continuous irregular cutting process can induce persistent slip bands (PSBs) in substrate surface, which would result in stress concentration and inhomogeneous deformation within grains.