Silicon speciation has recently gained interest in the oil and gas industry due to the impact of silicon species on hydrotreatment (HDT) catalysts. The determination of the chemical structure of silicon compounds appears as essential to limit silicon poisoning as to improve the lifetime of catalysts. To achieve a representative speciation of silicon in petroleum products, fresh samples of PDMS degradation under thermal cracking of hydrocarbons were produced using a pilot plant. The samples were carefully stored in a dewar containing liquid nitrogen (−195 °C) to minimize the possible evolution of silicon species and to allow their analysis in representative conditions. A complete analytical approach based on gas chromatography (GC) and mass spectrometry techniques (MS) was developed and applied to the samples produced at 500 °C. Moreover, to resolve coelutions observed by GC/TOFMS, GC–GC/TOFMS was successfully applied to obtain the mass spectrum of only one silicon compound. Combining the GC/MS mass spectrum giving access to the fragmentation of the compound and the raw formula and double bond equivalent (DBE) obtained by ESI-FT-ICR/MS, chemical structures were proposed. Almost molecules were strengthened by MSn.Cyclic siloxanes (Dn) were confirmed as the major compounds of PDMS thermal degradation even in the presence of hydrocarbons with a relative amount generally around 95% or above. No significant difference on the formation of Dn were observed according to the different operating conditions under thermal cracking of hydrocarbons. For the first time, several other silicon compounds present at trace levels (<5% of the total area) were characterized. α,ω-dihydroxy polydimethylsiloxanes, methylhydroxy cyclic siloxanes, (n + 1)oxasilabicyclo alcanes or bis(cyclosiloxanyl) siloxane, α-hydroxy, ω-methyl polysiloxanes and (n)oxasilabicyclo alcanes were preferentially formed in the presence of steam. Under evaluated coking or visbreaking conditions (long residence time without steam), other compounds were mainly characterized such as dimethoxy polysiloxanes, methyl(hydroperoxy) cyclic siloxanes, or ethoxy methyl cyclic siloxanes, linear polysiloxanes and methylpropyl cyclic siloxanes. Around one hundred silicon compounds were highlighted belonging to 12 different chemical families. The same repetition pattern (C2H6OSi), initially in PDMS, was present in all silicon compounds characterized in this study. Molecules with a number of silicon atoms ranging from 1 to 40 silicon atoms clearly demonstrated the occurrence of silicon in all petroleum cuts through very different chemical structures. This study shows that silicon species can distillate from gas fractions to the heavy petroleum cuts depending on their boiling points and chemical properties. These silicon species contain reactive groups (hydroxy, hydroperoxy, methoxy and ethoxy) which are able to react at the surface of HDT catalysts and cause a severe deactivation. Thus, these results appear as a crucial advance in progressing in the understanding of silicon poisoning.