The geometrical and electronic structures of a metastable phase of lead phthalocyanine (PbPc) films on graphite have been studied by combined use of low energy electron diffraction (LEED) and two-photon photoemission (2PPE) spectroscopy. In submonolayer (sub-ML) PbPc films on graphite, islands in a metastable phase are formed just after deposition, as we reported previously by use of photoelectron emission microscopy (PEEM) [I. Yamamoto, N. Matsuura, M. Mikamori, R. Yamamoto, T. Yamada, K. Miyakubo, N. Ueno, and T. Munakata, Surf. Sci. 602, 2232 (2008)]. On single crystalline graphite substrates, the metastable islands produce clearly discernible LEED spots. By comparing the unit cell with that of annealed 1 ML films, molecules in the metastable islands are standing upright with a molecular density 1.8 times higher than that in the well-ordered 1 ML films. The LEED spots for the sub-ML films disappear after annealing. The islands in the metastable phase are surrounded by areas of a two-dimensional (2D) gaslike phase composed of flat-lying molecules. The metastable islands melt into the 2D gas phase, consistent with the PEEM results. In 2PPE spectroscopy, the lowest unoccupied molecular orbital (LUMO) derived level of the metastable phase is clearly distinguishable from that of flat-lying molecules. By tracking the thermal annealing process of the films by 2PPE spectroscopy, we clarify the decay of the LUMO derived peak intensity, the work function shift, and the energy shifts of molecular states associated with the transition from the metastable phase to the 2D gas phase. With this, we demonstrate the complementary capabilities of LEED and 2PPE spectroscopy to probe phase transitions of organic films in a nondestructive manner.