Following consideration of the characteristics of high temperature, high pressure and high in-situ stress in ultra-deep sedimentary basins, together with the existence of hydrocarbon phase state transformation, hydrocarbon-water-rock interaction and rock mechanical property transition at those depths, the evaluation index system for hydrocarbon preservation was established. The physical leakage evaluation indexes can be divided into three categories: the dynamic efficiency indexes of micro-sealing, caprock integrity and natural gas diffusion. The chemical loss evaluation indexes can be divided into two categories: the thermochemical sulfate reduction (TSR) index in marine gypsum-bearing carbonate strata and the thermochemical oxidation of hydrocarbons (TOH) index in clastic strata. The slippage angle and overconsolidation ratio (OCR) are the key evaluation indexes in the evaluation of the integrity of shale caprocks. TSR intensity can be quantitatively calculated by use of the ZnPVT state parameter method. The TOH strength can be used to estimate the degree of hydrocarbon chemical loss, based on the TOH-related authigenic calcite cement content or the degree of negative δ13C of authigenic calcite. For the evaluation of ultra-deep preservation in specific areas, key indexes can be selected according to the local geological conditions, instead of all indexes needing to be evaluated for every scenario.