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Structural phase transformation and dislocation slip are two important deformation modes of monocrystalline silicon. In the present work, we elucidate mechanisms of inhomogeneous elastic-plastic transition in spherical nanoindentation of monocrystalline silicon by means of molecular dynamics simulations. The Stillinger-Weber potential is utilized to present simultaneous phase transformations and dislocation activities in the silicon nanoindentation. And a bond angle analysis-based method is proposed to quantitatively clarify silicon phases. The influence of crystallographic orientation on the silicon nanoindentation is further addressed. Our simulation results indicate that prior to the ‘‘Pop-In” event, Si(010) undergoes inelastic deformation accompanied by the phase transformation from the Si-I to the Si-III/ Si-XII, which is not occurred in Si(110) and Si(111). While the phase transformation from the Si-I to the bct-5 is the dominant mechanism of incipient plasticity for each crystallographic orientation, dislocation nucleation is also an operating deformation mode in the elastic-plastic transition of Si(010). Furthermore, interactions between phase transformations and dislocations are more pronounced in Si (010) than the other two crystallographic orientations.