Time-dependent phase transitions of closely packed alkanethiol self-assembled monolayers (SAMs) on Au(111) were investigated by scanning tunneling microscopy (STM). We report a new phase, the 6 x root3 superlattice, that exhibits deviations from the hexagonal packing arrangement formed through long-term rearrangement of the usual c(4 x 2) superlattice of alkanethiol SAMs. Our STM images show clearly systematic phase transitions with molecular-scale images from the c(4 x 2) phase to the 6 x root3 phase. This result implies that the monolayers in the c(4 x 2) phase are still in the nonequilibrium state, although it has been regarded to be in the equilibrium state in a number of previous studies. The striking implication in this study is to provide new features for closely packed alkanethiol SAMs for the first time.