This is the first study that employs large-scale atomistic simulations to examine the stress generation and deformation mechanisms of various Si nanopillars (SiNPs) during Li-ion insertion. First, a new robust and effective minimization approach is proposed to relax a lithiated amorphous SiNP (a-SiNP), which outperforms the known methods. Using this new method, our simulations are able to successfully capture the experimental morphological changes and volume expansions that SiNPs, hollow a-SiNPs, and solid crystalline SiNPs (c-SiNPs) experience upon maximum lithiation. These simulations enable us to selectively track the displacement of Si atoms and their atomic shear strain in the Li3.75Si alloy region, allowing us to observe the plastic flow and illustrate the atomistic mechanism of lithiation-induced deformation for various SiNPs for the first time. Based on the simulation results, a simple fracture mechanistic model is used to determine the fracture resistance of SiNPs, showing that the hollow a-SiNP is the optimal form of Si as an anode because it has the highest fracture resistance. The crack propagation simulation suggests that the preexisting dislocations in pristine c-Si can contribute toward the fracture of c-SiNPs during lithiation. These findings can guide the design of new Si-based anode geometries for the next-generation Li-ion batteries.