Abstract: The conventional biomarkers are limited due to the extremely high thermal stresses in ultra-deep hydrocarbon reservoirs. The diamondoid with cage structure has excellent thermal stability and is an effective tool for characterizing the ultra-deep hydrocarbon and linking its source. We investigated the distribution of diamondoids in ultra-deep reservoirs including black oils, volatile oils, and condensates. The source-related diamondoids indicate that crude oils are mainly sourced from marine siliceous shale. The bulk characteristics (e.g. color, density, Sat/Aro) of crude oils reveal the variations of thermal maturity: low maturity for black oils, moderate maturity for volatile oils, and high maturity for condensates. Based on regular variations in the thermal maturity of crude oils, the thermal evolution of diamondoids is characterized. The abundance of C1- and C2-alkylated diamantanes increases with increasing maturity, and hydrothermal activity may lead to an abnormal increase in the percentage of C3-alkylated adamantanes. Despite the higher thermal stability of 4-methyldiamantane (4-MD), a more sensitive change in relative abundance with maturity for 1-methyldiamantane (1-MD) among all methyldiamantanes (MDs) is observed. Ethyl diamondoids are thermally less stable and their derived indices can effectively indicate the thermal maturity of ultra-deep hydrocarbons. The applications of commonly maturity-related indices should be cautious (e.g. MDI), whereas the novel methyl-ethyl diamantane Index (MEDI) is highly recommended. The combination of high MAI values and low MEDI values most likely reflects the influence of late-charged light hydrocarbons. Overall, multiple charging and in-reservoir mixing of light hydrocarbons and oils with various maturities constrained the present phase states of ultra-deep oil reservoirs. This study gives a new perspective to understanding the fate of molecular evolution and phase states of hydrocarbons in the ultra-deep basins.