Hydrocarbon expulsion occurs only when pore fluid pressure due to hydrocarbon generation in source rock exceeds the force against migration in the adjacent carrier beds. Taking the Middle–Upper Ordovician carbonate source rock of Tarim Basin in China as an example, this paper proposes a method that identifies effective carbonate source rock based on the principles of mass balance. Data from the Well YW2 indicate that the Middle Ordovician Yijianfang Formation contains effective carbonate source rocks with low present-day TOC. Geological and geochemical analysis suggests that the hydrocarbons in the carbonate interval are likely self-generated and retained. Regular steranes from GC–MS analysis of oil extracts in this interval display similar features to those of the crude oil samples in Tabei area, indicating that the crude oil probably was migrated from the effective source rocks. By applying to other wells in the basin, the identified effective carbonate source rocks and non-source rock carbonates can be effectively identified and consistent with the actual exploration results, validating the method. Considering the contribution from the identified effective source rocks with low present-day TOC (TOCpd) is considered, the long-standing puzzle between the proved 3P oil reserves and estimated resources in the basin can be reasonably explained.