Scanning tunneling microscopy (STM) and spectroscopy (STS) were used to study the surface phase manipulation between c(4×2) and p(2×2) on the Si(100) surfaces at 6 K. We found that there is a correlation between the sample voltage range that induced p(2×2) (c(4×2)) and the energy position of the π^* (π) state with respect to the Fermi level. This suggests that electron injection into the π^* state caused the emergence of p(2×2), while the hole injection into π state retrieved the c(4×2) surfaces. Moreover, field emission from the STM tip and the subsequent STM observation confirmed that electron beam irradiation onto the Si(100) surfaces caused flip-flop motion of dimers. Such findings resolved recent controversy in the observations of the Si(100) surfaces at low temperatures using STM and low energy electron diffraction. We concluded that the c(4×2) structure is the most stable and the p(2×2) phase is a meta-stable structure.