Hybrid organic-inorganic system composed of iron porphyrin deposited on Si substrate was investigated by spectroscopic ellipsometry. A series of samples with (100) and (111)-oriented Si wafers and various acidity of aqueous solution of iron porphyrin deposited on Si substrates were fabricated and investigated. Experimental data were analysed in various models in order to reveal the general regularities of the hybrid system. It was determined that in hybrid samples, the mesostructures of iron porphyrin formed from both acid and base aqueous solutions possess similar electronic excitation bands. It was proposed that a major part of iron oxo-dimers were destroyed on the Si surface due to formation of the chemical bonds between Si substrate covered by native oxide and iron porphyrin.