Annual variance of carbon emissions and carbon leakage in the Natural Forest Protection Program (NFPP) was analyzed based on the calculation of carbon emissions from afforestation within the project boundary and carbon leakage out of the boundary in the first-stage (2000-2010) of the NFPP. Carbon emissions and carbon leakage were compared among the NFPP and its component regions, and variance of net carbon sequestration was characterized. The results showed that carbon emissions of the NFPP in the combined northwest and mid-west regions, the south region, the northeast region, and the whole NFPP region were 0.89, 1.47, 0.09, 2.45 Tg C, respectively. Meanwhile, carbon leakage from the above regions was 3.17, 3.11, 6.50, 12.78 Tg C, respectively. Spatial differences in program measures and carbon emission intensity were responsible for the differences in carbon emissions between various regions. Program measures showed that afforestation and corresponding forestry infrastructure construction were most prominent for the northwest/mid-west regions and the south region, while protection of young and mature forests was important in the northeast region. Accordingly, production and consumption of building materials were the main sources of carbon emissions for the former two regions, and consumption of fossil fuels was the main source for the latter region. Overall, in the first-stage of the NFPP, additional greenhouse gas emissions resulting from carbon emissions and carbon leakage totaled 15.23 Tg C, which counteracted 9.82% of the sequestered carbon in the program. Greenhouse gas emissions from the northwest/mid-west regions, the south region, and the northeast region could countervail 10.08%, 8.16%, and 11.24% of their carbon sequestration, respectively. Net carbon sequestration in the first-stage of the NFPP was 139.77 Tg C with an annual average of 12.71 Tg C/a. Therefore, carbon emissions and carbon leakage only played a minor role in neutralizing carbon benefits, and the first-stage of the NFPP contributed significantly to greenhouse gas emission reduction in China as well as global climate warming mitigation. Potential routes of greenhouse gas emission reduction include reasonable planning and avoidance of impulsive or reckless construction.