We have studied the molecular orbitals and arrangements of N,N'-dimethylperylene-3,4,9,10-bis(dicarboximide) (Me-PTC) molecules deposited on clean Si(100)2 x 1 and the H-terminated Si(100) surfaces on the basis of metastable de-excitation spectroscopy (MDS) experiments. The charge density of the second layer Me-PTC molecular orbitals differs somewhat from that of the first layer. The desorption temperature of Me-PTC from H-terminated Si surface is lower than that from clean Si. This is because Me-PTC molecules combine weakly with the H-terminated Si substrate.