In cyclic nanoindentation of single-crystal silicon, an interesting phenomenon of a secondary pop-out event that closely follows the first pop-out event but with a larger critical load than the first is presented. Cyclic nanoindentation experiments under various loading/unloading rates and various maximum indentation loads were performed to verify the generality of the phenomenon of two pop-out events. Raman spectroscopy results indicate that the secondary pop-out does not induce any new phase, and the dominated end phases after the two pop-out events are still a mixture of Si-XII/Si-III phases. According to average contact pressure analysis, the phase transformation paths and the formation mechanism for the secondary pop-out event are discussed from the viewpoint of crystal nucleation and growth. The results indicate that phase transformations from the Si-I phase to Si-XII/Si-III phases are completed by two pop-out events in two adjacent indentation cycles, and the Si-XII/Si-III phases formed in previous indentation cycles strongly affect the phase transformations in subsequent loading/unloading processes.