The system In-[perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA)] on MoS2, prepared by the sequential evaporation of PTCDA and In on a cleaved MoS2 surface, was studied by low energy electron diffraction. The result indicates that reaction products form an ordered structure on the MoS2 surface. From the analysis of the diffraction pattern, the presence of six symmetry-equivalent domains of an oblique unit cell of In-PTCDA species results with the dimensions of 9.5 Å, 16.3 Å, and an enclosed angle of 80.2°. In addition, splitting in two domains by a mirror plane exists with the rotation angle R=±10.8° with respect to each of the three equivalent surface crystal axes of the MoS2 substrate. The new structure is explained by assuming that four In atoms are chemically bonded to the four carbonyl groups of the PTCDA molecules. Furthermore, it is concluded that the In4PTCDA species become tilted after a chemical reaction between the PTCDA molecules and the In atoms, which is in agreement with results previously obtained by angle-resolved ultraviolet photoemission experiments.