The invention discloses a carbon emission accounting method and system for a thermal power generation unit. The method comprises the following steps: collecting a plurality of sets of data of flue gasemitted by the thermal power generation unit in a preset accounting period, wherein each set of data includes: flue gas volume flow data and target greenhouse gas concentration data in the flue gas;calculating the emissions of the target greenhouse gases corresponding to each set of data within the preset accounting period, and using each set of data separately; according to the preset algorithmand the target greenhouse gas emission corresponding to each group of data, evaluating and calculating the reliability of each group of collected data to judge whether the collected data accord withthe preset reliability index; if so, calculating the average value of the target greenhouse gas emissions corresponding to each group of data, and taking the calculated average value as the carbon emission accounting value of the thermal power generation unit in the accounting period. The method and system realize the accurate, rationalization and uniqueness of greenhouse gas emission accounting of thermal power generating units.