Carbon emission accounting is an important basis for achieving greenhouse gas emission reduction goals. Clarifying the change of carbon emission intensity and evaluating the effectiveness of carbon emission reduction is vital to implement low-carbon development measures from the point of view of the Major Function Oriented Zones (MFOZs). This study took Shanxi Province, a typical province with high carbon economy, as the research object. In the MFOZs, the BP neural network model was adopted to build a carbon emission accounting model based on the district level carbon emission, population, GDP, the sum of digital number, vegetation coverage, and urbanization level. Using the methods of spatial auto-correlation analysis, Dagum Gini coefficient, and time propensity rate, this paper analyzed the carbon emission spatio-temporal characteristics and its regional differences, and evaluated the effectiveness of carbon emission reduction of the MFOZs in Shanxi Province. The results showed that:(1) from the perspective of time, the carbon emissions of the MFOZs presented an increasing trend from 2006 to 2020. The growth rate was in the order of the key development zone (48.08%)>the main agricultural production zone (38.13%)>the key ecological functional zone (33.95%), which was significantly related to the functional positioning and industrial structure of the MFOZs. (2) In terms of spatial evolution, the spatial agglomeration characteristics of the MFOZs were linked to the unique topography of Shanxi Province. The spatial agglomeration pattern of the key development zone was relatively stable, while the main agricultural production zone and the key ecological functional zone were not significant. (3) The overall differences of carbon emissions in Shanxi Province presented a downward trend, and the total Gini coefficient decreased from 0.505 in 2006 to 0.498 in 2020, with an averagely annual decline of 0.102%. The difference among the MFOZs, especially the difference between the key development zone and the key ecological functional zone, was the main source of the overall difference. (4) The carbon emission intensity of the MFOZs exhibited on the decline, and the effectiveness of carbon emission reduction of the key development zone was significantly better than the main agricultural production zone and the key ecological functional zone. Based on the analysis of the carbon emission and combined with functional positioning of the MFOZs, the targeted measures for emission reduction and low-carbon development of the MFOZs were proposed. It is of scientific reference value to formulate and implement the differentiated energy saving and emission reduction policies for the Chinese energy resource-based provinces.